Raspbian Package Auto-Building

Build log for python-biopython (1.81+dfsg-2) on armhf

python-biopython1.81+dfsg-2armhf → 2023-11-14 07:12:25

sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023

+==============================================================================+
| python-biopython 1.81+dfsg-2 (armhf)         Tue, 14 Nov 2023 06:54:16 +0000 |
+==============================================================================+

Package: python-biopython
Version: 1.81+dfsg-2
Source Version: 1.81+dfsg-2
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-24294010-01d2-45ae-b08a-751d102d18f2' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/python-biopython-qkNHAu/resolver-k3dQi5' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.2 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.9 MB]
Fetched 29.2 MB in 5s (5603 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'python-biopython' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-biopython.git
Please use:
git clone https://salsa.debian.org/med-team/python-biopython.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 11.5 MB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main python-biopython 1.81+dfsg-2 (dsc) [3377 B]
Get:2 http://172.17.4.1/private trixie-staging/main python-biopython 1.81+dfsg-2 (tar) [11.5 MB]
Get:3 http://172.17.4.1/private trixie-staging/main python-biopython 1.81+dfsg-2 (diff) [20.6 kB]
Fetched 11.5 MB in 1s (8470 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-biopython-qkNHAu/python-biopython-1.81+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-biopython-qkNHAu' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-numpy, flex, python3-reportlab (>= 4.0.4-1~), hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-numpy, flex, python3-reportlab (>= 4.0.4-1~), hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [615 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [1505 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1134 B]
Fetched 3254 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev blt bsdextrautils bwa clustalo
  clustalw debhelper dh-autoreconf dh-python dh-strip-nondeterminism dialign
  dpkg-dev dssp dwz emboss emboss-data emboss-lib fasttree file flex
  fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
  fonts-lmodern fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript
  groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common
  imagemagick-6.q16 intltool-debian libabsl20220623 libaom3 libapache-pom-java
  libarchive-zip-perl libargtable2-0 libavahi-client3 libavahi-common-data
  libavahi-common3 libavif16 libblas3 libboost-regex1.74.0 libbrotli1 libbsd0
  libcairo2 libcifpp-data libcifpp5 libcommons-logging-java
  libcommons-parent-java libcups2 libcurl3-gnutls libdav1d6 libdbus-1-3
  libde265-0 libdebhelper-perl libdeflate0 libdpkg-perl libelf1 libexpat1
  libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl
  libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0
  libgav1-1 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgs-common
  libgs10 libgs10-common libharfbuzz0b libheif-plugin-dav1d
  libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhts3 libhtscodecs2 libice6
  libicu72 libidn12 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0
  libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc
  libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 liblerc4
  liblmdb0 liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-7
  libmagickwand-6.q16-7 libmariadb3 libmbedcrypto7 libmbedtls14 libmbedx509-1
  libncurses6 libnetpbm11 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1
  libpdfbox-java libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libpq5
  libpsl5 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
  libqhull-r8.0 libraqm0 librav1e0 libraw23 librtmp1 libsharpyuv0 libsm6
  libssh2-1 libsub-override-perl libsvtav1enc1d1 libsynctex2 libtcl8.6
  libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libuchardet0 libwebp7
  libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2
  libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6 libyuv0 libzzip-0-13
  m4 mafft mailcap man-db mariadb-common media-types mime-support mysql-common
  ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank
  preview-latex-style probcons python-matplotlib-data python3 python3-all
  python3-all-dev python3-appdirs python3-attr python3-brotli python3-cairo
  python3-contourpy python3-cycler python3-dateutil python3-decorator
  python3-dev python3-distutils python3-fonttools python3-freetype python3-fs
  python3-isodate python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4
  python3-matplotlib python3-minimal python3-mmtf python3-mpmath
  python3-msgpack python3-mysqldb python3-networkx python3-numpy
  python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources
  python3-psycopg2 python3-pygments python3-pyparsing python3-rdflib
  python3-reportlab python3-rlpycairo python3-scipy python3-setuptools
  python3-six python3-sympy python3-tk python3-tz python3-ufolib2
  python3-unittest2 python3.11 python3.11-dev python3.11-minimal samtools
  sensible-utils t-coffee t1utils tex-common texlive-base texlive-binaries
  texlive-fonts-recommended texlive-latex-base texlive-latex-extra
  texlive-latex-recommended texlive-pictures tk8.6-blt2.5 ucf unicode-data
  wise wise-data x11-common xdg-utils xfonts-encodings xfonts-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc blt-demo clustalx seaview
  dh-make flit python3-build python3-installer python3-wheel debian-keyring
  emboss-doc emboss-test embassy bison flex-doc fonts-freefont-otf
  | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev
  libgettextpo-dev groff hevea-doc imagemagick-doc autotrace cups-bsd | lpr
  | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps
  libwmf-bin mplayer povray radiance sane-utils transfig ufraw-batch
  libavalon-framework-java libcommons-logging-java-doc
  libexcalibur-logkit-java liblog4j1.2-java cups-common git bzr libfftw3-bin
  libfftw3-dev libgd-tools low-memory-monitor libheif-plugin-ffmpegdec
  libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec
  libheif-plugin-j2kenc libheif-plugin-rav1e libheif-plugin-svtenc
  libjs-jquery-ui-docs liblcms2-utils libmagickcore-6.q16-7-extra tcl8.6 tk8.6
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho
  | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic
  fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra python3-doc
  python3-venv python-attr-doc python-cycler-doc python-lxml-doc
  cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 inkscape ipython3
  librsvg2-common python3-cairocffi python3-gi python3-gi-cairo
  python3-gobject python3-pyqt5 python3-sip python3-tornado
  texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server
  | virtual-mysql-server gfortran python3-pytest python-pil-doc
  python-psycopg2-doc python-pygments-doc ttf-bitstream-vera
  python-pyparsing-doc python-rdflib-doc pdf-viewer python3-egenix-mxtexttools
  python-reportlab-doc python-scipy-doc python-setuptools-doc
  texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.11-venv
  python3.11-doc binfmt-support cwltool boxshade t-coffee-examples perl-tk
  xpdf | pdf-viewer xzdec texlive-binaries-sse2 texlive-fonts-recommended-doc
  texlive-latex-base-doc wp2latex icc-profiles libfile-which-perl
  texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc
  texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex
  wise-doc
Recommended packages:
  libalgorithm-merge-perl primer3 libfl-dev curl | wget | lynx
  libmagickcore-6.q16-7-extra ca-certificates dbus libfile-fcntllock-perl
  libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs
  fonts-droid-fallback libheif-plugin-aomenc libheif-plugin-x265
  javascript-common gsfonts libgpm2 publicsuffix libltdl-dev blast2
  libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 python3-html5lib
  python3-gdal python3-pydot python3-pygraphviz python3-yaml python3-olefile
  python3-sparqlwrapper isympy-common amap-align dialign-tx fsa kalign
  libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align
  lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl
  texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl
  libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev blt bsdextrautils bwa clustalo
  clustalw debhelper dh-autoreconf dh-python dh-strip-nondeterminism dialign
  dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config
  fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lmodern
  fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea
  hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16
  intltool-debian libabsl20220623 libaom3 libapache-pom-java
  libarchive-zip-perl libargtable2-0 libavahi-client3 libavahi-common-data
  libavahi-common3 libavif16 libblas3 libboost-regex1.74.0 libbrotli1 libbsd0
  libcairo2 libcifpp-data libcifpp5 libcommons-logging-java
  libcommons-parent-java libcups2 libcurl3-gnutls libdav1d6 libdbus-1-3
  libde265-0 libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java
  libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgd3
  libgfortran5 libglib2.0-0 libgraphite2-3 libgs-common libgs10 libgs10-common
  libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1
  libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu72 libidn12 libijs-0.35
  libimagequant0 libjbig0 libjbig2dec0 libjpeg62-turbo libjs-jquery
  libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3
  liblbfgsb0 liblcms2-2 liblerc4 liblmdb0 liblqr-1-0 libltdl7 libmagic-mgc
  libmagic1 libmagickcore-6.q16-7 libmagickwand-6.q16-7 libmariadb3
  libmbedcrypto7 libmbedtls14 libmbedx509-1 libncurses6 libnetpbm11
  libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java
  libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libpq5 libpsl5
  libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
  libqhull-r8.0 libraqm0 librav1e0 libraw23 librtmp1 libsharpyuv0 libsm6
  libssh2-1 libsub-override-perl libsvtav1enc1d1 libsynctex2 libtcl8.6
  libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libuchardet0 libwebp7
  libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2
  libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6 libyuv0 libzzip-0-13
  m4 mafft mailcap man-db mariadb-common media-types mime-support mysql-common
  ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank
  preview-latex-style probcons python-matplotlib-data python3 python3-all
  python3-all-dev python3-appdirs python3-attr python3-brotli python3-cairo
  python3-contourpy python3-cycler python3-dateutil python3-decorator
  python3-dev python3-distutils python3-fonttools python3-freetype python3-fs
  python3-isodate python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4
  python3-matplotlib python3-minimal python3-mmtf python3-mpmath
  python3-msgpack python3-mysqldb python3-networkx python3-numpy
  python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources
  python3-psycopg2 python3-pygments python3-pyparsing python3-rdflib
  python3-reportlab python3-rlpycairo python3-scipy python3-setuptools
  python3-six python3-sympy python3-tk python3-tz python3-ufolib2
  python3-unittest2 python3.11 python3.11-dev python3.11-minimal samtools
  sbuild-build-depends-main-dummy sensible-utils t-coffee t1utils tex-common
  texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base
  texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5
  ucf unicode-data wise wise-data x11-common xdg-utils xfonts-encodings
  xfonts-utils zlib1g-dev
The following packages will be upgraded:
  dpkg-dev libdpkg-perl
2 upgraded, 270 newly installed, 0 to remove and 12 not upgraded.
1 not fully installed or removed.
Need to get 303 MB/305 MB of archives.
After this operation, 1450 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1112 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf flex armhf 2.6.4-8.2 [391 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libpng16-16 armhf 1.6.40-2 [258 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libfreetype6 armhf 2.13.2+dfsg-1 [366 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libfontenc1 armhf 1:1.1.4-1 [22.3 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf xfonts-utils armhf 1:7.7+6 [82.5 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf fonts-urw-base35 all 20200910-7 [10.8 MB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf fontconfig-config armhf 2.14.2-6 [316 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libfontconfig1 armhf 2.14.2-6 [367 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libsharpyuv0 armhf 1.3.2-0.3 [106 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libdav1d6 armhf 1.2.1-2+rpi1 [214 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-dav1d armhf 1.17.1-1 [9168 B]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libde265-0 armhf 1.0.11-1+rpi1+b1 [137 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-libde265 armhf 1.17.1-1 [12.1 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libheif1 armhf 1.17.1-1 [229 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libjbig0 armhf 2.1-6.1 [27.0 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf liblcms2-2 armhf 2.14-2 [124 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libglib2.0-0 armhf 2.78.1-2 [1257 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.1 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libltdl7 armhf 2.4.7-7 [390 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libopenjp2-7 armhf 2.5.0-2 [164 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libraw23 armhf 0.21.1-7+rpi1 [363 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf liblerc4 armhf 4.0.0+ds-3 [133 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libwebp7 armhf 1.3.2-0.3 [261 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libtiff6 armhf 4.5.1+git230720-1 [298 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libwebpdemux2 armhf 1.3.2-0.3 [106 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libwebpmux3 armhf 1.3.2-0.3 [116 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.7-1 [328 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.7-1 [729 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf imagemagick-6-common all 8:6.9.12.98+dfsg1-3 [66.6 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libmagickcore-6.q16-7 armhf 8:6.9.12.98+dfsg1-3 [1514 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libmagickwand-6.q16-7 armhf 8:6.9.12.98+dfsg1-3 [285 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf poppler-data all 0.4.12-1 [1601 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.6-3 [800 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.6-3 [1674 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf mailcap all 3.70+nmu1 [32.0 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.6-3 [1679 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.6-3 [586 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:60 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-5 [80.8 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-13 [156 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf ucf all 3.0043+nmu1 [55.2 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libtcl8.6 armhf 8.6.13+dfsg-2 [904 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libxft2 armhf 2.3.6-1 [53.7 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libtk8.6 armhf 8.6.13-2 [680 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-4.1 [477 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf blt armhf 2.5.3+dfsg-4.1 [14.9 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf bwa armhf 0.7.17-7 [196 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libargtable2-0 armhf 13-1.1 [15.9 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf clustalo armhf 1.2.4-7 [222 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf clustalw armhf 2.1+lgpl-7 [229 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.7 [82.1 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.7 [956 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf python3-distutils all 3.11.5-1 [131 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf python3-pkg-resources all 68.1.2-2 [241 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf python3-setuptools all 68.1.2-2 [468 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf dh-python all 6.20231107 [107 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf dialign armhf 2.2.1-11 [134 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74.0 armhf 1.74.0+ds1-23 [421 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libcifpp-data all 5.0.7.1-3 [452 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libcifpp5 armhf 5.0.7.1-3 [674 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf dssp armhf 4.2.2-2 [587 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libaom3 armhf 3.7.0-1 [1387 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libabsl20220623 armhf 20220623.1-3 [356 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf libgav1-1 armhf 0.18.0-1+rpi1+b1 [285 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf librav1e0 armhf 0.6.6-3+rpi1 [548 kB]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libsvtav1enc1d1 armhf 1.7.0+dfsg-2 [884 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libyuv0 armhf 0.0~git20230907.cbfb661-1 [82.6 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libavif16 armhf 1.0.1-2 [93.4 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libxpm4 armhf 1:3.5.17-1 [49.3 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf libgd3 armhf 2.3.3-9+b1 [102 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf libhpdf-2.3.0 armhf 2.3.0+dfsg-1 [330 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf mysql-common all 5.8+1.1.0 [6636 B]
Get:121 http://172.17.4.1/private trixie-staging/main armhf mariadb-common all 1:10.11.3-1+rpi1 [24.1 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf libmariadb3 armhf 1:10.11.3-1+rpi1 [154 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libpq5 armhf 16.0-2 [193 kB]
Get:124 http://172.17.4.1/private trixie-staging/main armhf emboss-lib armhf 6.6.0+dfsg-12 [2587 kB]
Get:125 http://172.17.4.1/private trixie-staging/main armhf emboss-data all 6.6.0+dfsg-12 [61.1 MB]
Get:126 http://172.17.4.1/private trixie-staging/main armhf emboss armhf 6.6.0+dfsg-12 [1021 kB]
Get:127 http://172.17.4.1/private trixie-staging/main armhf fasttree armhf 2.1.11-2 [158 kB]
Get:128 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-extra all 2.37-8 [1792 kB]
Get:129 http://172.17.4.1/private trixie-staging/main armhf fonts-lmodern all 2.005-1 [4540 kB]
Get:130 http://172.17.4.1/private trixie-staging/main armhf fonts-lyx all 2.3.7-1 [186 kB]
Get:131 http://172.17.4.1/private trixie-staging/main armhf libgs-common all 10.02.0~dfsg-2 [149 kB]
Get:132 http://172.17.4.1/private trixie-staging/main armhf libgs10-common all 10.02.0~dfsg-2 [475 kB]
Get:133 http://172.17.4.1/private trixie-staging/main armhf libavahi-common-data armhf 0.8-13 [111 kB]
Get:134 http://172.17.4.1/private trixie-staging/main armhf libavahi-common3 armhf 0.8-13 [40.1 kB]
Get:135 http://172.17.4.1/private trixie-staging/main armhf libdbus-1-3 armhf 1.14.10-3 [177 kB]
Get:136 http://172.17.4.1/private trixie-staging/main armhf libavahi-client3 armhf 0.8-13 [42.6 kB]
Get:137 http://172.17.4.1/private trixie-staging/main armhf libcups2 armhf 2.4.7-1 [206 kB]
Get:138 http://172.17.4.1/private trixie-staging/main armhf libidn12 armhf 1.41-1+b1 [77.0 kB]
Get:139 http://172.17.4.1/private trixie-staging/main armhf libijs-0.35 armhf 0.35-15.1 [13.2 kB]
Get:140 http://172.17.4.1/private trixie-staging/main armhf libjbig2dec0 armhf 0.19-3+b2 [58.6 kB]
Get:141 http://172.17.4.1/private trixie-staging/main armhf libpaper1 armhf 1.1.29 [11.9 kB]
Get:142 http://172.17.4.1/private trixie-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:143 http://172.17.4.1/private trixie-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:144 http://172.17.4.1/private trixie-staging/main armhf libxt6 armhf 1:1.2.1-1.1 [155 kB]
Get:145 http://172.17.4.1/private trixie-staging/main armhf libgs10 armhf 10.02.0~dfsg-2 [2075 kB]
Get:146 http://172.17.4.1/private trixie-staging/main armhf ghostscript armhf 10.02.0~dfsg-2 [50.6 kB]
Get:147 http://172.17.4.1/private trixie-staging/main armhf libnetpbm11 armhf 2:11.03.06-1 [158 kB]
Get:148 http://172.17.4.1/private trixie-staging/main armhf netpbm armhf 2:11.03.06-1 [1815 kB]
Get:149 http://172.17.4.1/private trixie-staging/main armhf tex-common all 6.18 [32.5 kB]
Get:150 http://172.17.4.1/private trixie-staging/main armhf libpaper-utils armhf 1.1.29 [8416 B]
Get:151 http://172.17.4.1/private trixie-staging/main armhf libkpathsea6 armhf 2023.20230311.66589-6 [144 kB]
Get:152 http://172.17.4.1/private trixie-staging/main armhf libptexenc1 armhf 2023.20230311.66589-6 [42.4 kB]
Get:153 http://172.17.4.1/private trixie-staging/main armhf libsynctex2 armhf 2023.20230311.66589-6 [48.0 kB]
Get:154 http://172.17.4.1/private trixie-staging/main armhf libtexlua53-5 armhf 2023.20230311.66589-6 [82.4 kB]
Get:155 http://172.17.4.1/private trixie-staging/main armhf t1utils armhf 1.41-4 [52.3 kB]
Get:156 http://172.17.4.1/private trixie-staging/main armhf libpixman-1-0 armhf 0.42.2-1 [461 kB]
Get:157 http://172.17.4.1/private trixie-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:158 http://172.17.4.1/private trixie-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:159 http://172.17.4.1/private trixie-staging/main armhf libcairo2 armhf 1.18.0-1 [425 kB]
Get:160 http://172.17.4.1/private trixie-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:161 http://172.17.4.1/private trixie-staging/main armhf libharfbuzz0b armhf 8.0.1-1 [2098 kB]
Get:162 http://172.17.4.1/private trixie-staging/main armhf libpotrace0 armhf 1.16-2 [23.6 kB]
Get:163 http://172.17.4.1/private trixie-staging/main armhf libteckit0 armhf 2.5.11+ds1-1 [256 kB]
Get:164 http://172.17.4.1/private trixie-staging/main armhf libxmu6 armhf 2:1.1.3-3 [52.0 kB]
Get:165 http://172.17.4.1/private trixie-staging/main armhf libxaw7 armhf 2:1.0.14-1 [165 kB]
Get:166 http://172.17.4.1/private trixie-staging/main armhf libxi6 armhf 2:1.8-1 [78.1 kB]
Get:167 http://172.17.4.1/private trixie-staging/main armhf libzzip-0-13 armhf 0.13.72+dfsg.1-1.1 [54.3 kB]
Get:168 http://172.17.4.1/private trixie-staging/main armhf texlive-binaries armhf 2023.20230311.66589-6 [5571 kB]
Get:169 http://172.17.4.1/private trixie-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:170 http://172.17.4.1/private trixie-staging/main armhf texlive-base all 2023.20231007-1 [22.0 MB]
Get:171 http://172.17.4.1/private trixie-staging/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB]
Get:172 http://172.17.4.1/private trixie-staging/main armhf imagemagick-6.q16 armhf 8:6.9.12.98+dfsg1-3 [290 kB]
Get:173 http://172.17.4.1/private trixie-staging/main armhf imagemagick armhf 8:6.9.12.98+dfsg1-3 [19.0 kB]
Get:174 http://172.17.4.1/private trixie-staging/main armhf hevea armhf 2.36-2 [1685 kB]
Get:175 http://172.17.4.1/private trixie-staging/main armhf libapache-pom-java all 29-2 [5276 B]
Get:176 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:177 http://172.17.4.1/private trixie-staging/main armhf libcommons-parent-java all 56-1 [10.8 kB]
Get:178 http://172.17.4.1/private trixie-staging/main armhf libcommons-logging-java all 1.2-4 [60.2 kB]
Get:179 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:180 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:181 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:182 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:183 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.4.0-2+rpi1 [358 kB]
Get:184 http://172.17.4.1/private trixie-staging/main armhf libexpat1-dev armhf 2.5.0-2 [130 kB]
Get:185 http://172.17.4.1/private trixie-staging/main armhf libfontbox-java all 1:1.8.16-4 [211 kB]
Get:186 http://172.17.4.1/private trixie-staging/main armhf libfribidi0 armhf 1.0.13-3 [69.9 kB]
Get:187 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-5+rpi1 [247 kB]
Get:188 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.5.2-1 [60.0 kB]
Get:189 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.18+ds-1 [380 kB]
Get:190 http://172.17.4.1/private trixie-staging/main armhf libimagequant0 armhf 2.17.0-1 [28.0 kB]
Get:191 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:192 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:193 http://172.17.4.1/private trixie-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:194 http://172.17.4.1/private trixie-staging/main armhf libjs-sphinxdoc all 7.2.6-2 [149 kB]
Get:195 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:196 http://172.17.4.1/private trixie-staging/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1 [24.4 kB]
Get:197 http://172.17.4.1/private trixie-staging/main armhf liblmdb0 armhf 0.9.31-1 [37.4 kB]
Get:198 http://172.17.4.1/private trixie-staging/main armhf libmbedcrypto7 armhf 2.28.5-1 [243 kB]
Get:199 http://172.17.4.1/private trixie-staging/main armhf libmbedx509-1 armhf 2.28.5-1 [126 kB]
Get:200 http://172.17.4.1/private trixie-staging/main armhf libmbedtls14 armhf 2.28.5-1 [156 kB]
Get:201 http://172.17.4.1/private trixie-staging/main armhf libncurses6 armhf 6.4+20231016-1 [80.0 kB]
Get:202 http://172.17.4.1/private trixie-staging/main armhf libpdfbox-java all 1:1.8.16-4 [5527 kB]
Get:203 http://172.17.4.1/private trixie-staging/main armhf libpython3.11 armhf 3.11.6-3 [1662 kB]
Get:204 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:205 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-dev armhf 3.11.6-3 [3271 kB]
Get:206 http://172.17.4.1/private trixie-staging/main armhf libpython3-dev armhf 3.11.4-5 [9432 B]
Get:207 http://172.17.4.1/private trixie-staging/main armhf libpython3-all-dev armhf 3.11.4-5 [1068 B]
Get:208 http://172.17.4.1/private trixie-staging/main armhf libqhull-r8.0 armhf 2020.2-6 [216 kB]
Get:209 http://172.17.4.1/private trixie-staging/main armhf libraqm0 armhf 0.10.1-1 [11.7 kB]
Get:210 http://172.17.4.1/private trixie-staging/main armhf libxslt1.1 armhf 1.1.35-1 [221 kB]
Get:211 http://172.17.4.1/private trixie-staging/main armhf mafft armhf 7.505-1 [734 kB]
Get:212 http://172.17.4.1/private trixie-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB]
Get:213 http://172.17.4.1/private trixie-staging/main armhf ncbi-blast+ armhf 2.12.0+ds-4 [10.0 MB]
Get:214 http://172.17.4.1/private trixie-staging/main armhf phylip armhf 1:3.697+dfsg-2 [683 kB]
Get:215 http://172.17.4.1/private trixie-staging/main armhf prank armhf 0.0.170427+dfsg-3 [298 kB]
Get:216 http://172.17.4.1/private trixie-staging/main armhf preview-latex-style all 12.2-1 [201 kB]
Get:217 http://172.17.4.1/private trixie-staging/main armhf probcons armhf 1.12-14 [100 kB]
Get:218 http://172.17.4.1/private trixie-staging/main armhf python-matplotlib-data all 3.6.3-1 [2744 kB]
Get:219 http://172.17.4.1/private trixie-staging/main armhf python3-all armhf 3.11.4-5 [1060 B]
Get:220 http://172.17.4.1/private trixie-staging/main armhf python3.11-dev armhf 3.11.6-3 [508 kB]
Get:221 http://172.17.4.1/private trixie-staging/main armhf python3-dev armhf 3.11.4-5 [26.2 kB]
Get:222 http://172.17.4.1/private trixie-staging/main armhf python3-all-dev armhf 3.11.4-5 [1068 B]
Get:223 http://172.17.4.1/private trixie-staging/main armhf python3-appdirs all 1.4.4-4 [12.5 kB]
Get:224 http://172.17.4.1/private trixie-staging/main armhf python3-attr all 23.1.0-2 [67.1 kB]
Get:225 http://172.17.4.1/private trixie-staging/main armhf python3-brotli armhf 1.0.9-2+b3 [278 kB]
Get:226 http://172.17.4.1/private trixie-staging/main armhf python3-cairo armhf 1.24.0-3 [103 kB]
Get:227 http://172.17.4.1/private trixie-staging/main armhf python3-numpy armhf 1:1.24.2-1 [3826 kB]
Get:228 http://172.17.4.1/private trixie-staging/main armhf python3-contourpy armhf 1.0.7-1 [141 kB]
Get:229 http://172.17.4.1/private trixie-staging/main armhf python3-cycler all 0.11.0-1 [8020 B]
Get:230 http://172.17.4.1/private trixie-staging/main armhf python3-six all 1.16.0-4 [17.5 kB]
Get:231 http://172.17.4.1/private trixie-staging/main armhf python3-dateutil all 2.8.2-3 [78.4 kB]
Get:232 http://172.17.4.1/private trixie-staging/main armhf python3-decorator all 5.1.1-5 [15.1 kB]
Get:233 http://172.17.4.1/private trixie-staging/main armhf python3-scipy armhf 1.10.1-2+rpi1 [13.6 MB]
Get:234 http://172.17.4.1/private trixie-staging/main armhf python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB]
Get:235 http://172.17.4.1/private trixie-staging/main armhf python3-mpmath all 1.2.1-2 [418 kB]
Get:236 http://172.17.4.1/private trixie-staging/main armhf python3-sympy all 1.12-6 [3868 kB]
Get:237 http://172.17.4.1/private trixie-staging/main armhf python3-tz all 2023.3.post1-1 [30.8 kB]
Get:238 http://172.17.4.1/private trixie-staging/main armhf python3-fs all 2.4.16-2 [95.2 kB]
Get:239 http://172.17.4.1/private trixie-staging/main armhf python3-lxml armhf 4.9.3-1 [1039 kB]
Get:240 http://172.17.4.1/private trixie-staging/main armhf python3-lz4 armhf 4.0.2+dfsg-1+b1 [23.9 kB]
Get:241 http://172.17.4.1/private trixie-staging/main armhf unicode-data all 15.1.0-1 [8547 kB]
Get:242 http://172.17.4.1/private trixie-staging/main armhf python3-fonttools armhf 4.38.0-1 [1047 kB]
Get:243 http://172.17.4.1/private trixie-staging/main armhf python3-freetype all 2.4.0-1 [80.3 kB]
Get:244 http://172.17.4.1/private trixie-staging/main armhf python3-isodate all 0.6.1-1 [25.3 kB]
Get:245 http://172.17.4.1/private trixie-staging/main armhf python3-kiwisolver armhf 1.4.4-1 [52.3 kB]
Get:246 http://172.17.4.1/private trixie-staging/main armhf python3-pil armhf 10.0.0-1 [437 kB]
Get:247 http://172.17.4.1/private trixie-staging/main armhf python3-tk armhf 3.11.5-1 [95.9 kB]
Get:248 http://172.17.4.1/private trixie-staging/main armhf python3-pil.imagetk armhf 10.0.0-1 [75.2 kB]
Get:249 http://172.17.4.1/private trixie-staging/main armhf python3-pyparsing all 3.1.1-1 [145 kB]
Get:250 http://172.17.4.1/private trixie-staging/main armhf python3-packaging all 23.1-1 [37.4 kB]
Get:251 http://172.17.4.1/private trixie-staging/main armhf python3-matplotlib armhf 3.6.3-1 [7453 kB]
Get:252 http://172.17.4.1/private trixie-staging/main armhf python3-msgpack armhf 1.0.3-3 [61.7 kB]
Get:253 http://172.17.4.1/private trixie-staging/main armhf python3-mmtf all 1.1.3-1 [17.0 kB]
Get:254 http://172.17.4.1/private trixie-staging/main armhf python3-mysqldb armhf 1.4.6-2+b1 [46.8 kB]
Get:255 http://172.17.4.1/private trixie-staging/main armhf python3-networkx all 2.8.8-1 [1425 kB]
Get:256 http://172.17.4.1/private trixie-staging/main armhf python3-psycopg2 armhf 2.9.6-3 [108 kB]
Get:257 http://172.17.4.1/private trixie-staging/main armhf python3-pygments all 2.15.1+dfsg-1 [817 kB]
Get:258 http://172.17.4.1/private trixie-staging/main armhf python3-rdflib all 6.1.1-2 [383 kB]
Get:259 http://172.17.4.1/private trixie-staging/main armhf python3-rlpycairo all 0.3.0-3 [9904 B]
Get:260 http://172.17.4.1/private trixie-staging/main armhf python3-reportlab all 4.0.4-11 [668 kB]
Get:261 http://172.17.4.1/private trixie-staging/main armhf python3-unittest2 all 1.1.0-9 [75.8 kB]
Get:262 http://172.17.4.1/private trixie-staging/main armhf samtools armhf 1.18-1 [587 kB]
Get:263 http://172.17.4.1/private trixie-staging/main armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [786 kB]
Get:264 http://172.17.4.1/private trixie-staging/main armhf texlive-fonts-recommended all 2023.20231007-1 [4990 kB]
Get:265 http://172.17.4.1/private trixie-staging/main armhf texlive-latex-base all 2023.20231007-1 [1239 kB]
Get:266 http://172.17.4.1/private trixie-staging/main armhf texlive-latex-recommended all 2023.20231007-1 [8835 kB]
Get:267 http://172.17.4.1/private trixie-staging/main armhf texlive-pictures all 2023.20231007-1 [15.9 MB]
Get:268 http://172.17.4.1/private trixie-staging/main armhf texlive-latex-extra all 2023.20231007-2 [19.5 MB]
Get:269 http://172.17.4.1/private trixie-staging/main armhf wise-data all 2.4.1-23 [78.2 kB]
Get:270 http://172.17.4.1/private trixie-staging/main armhf wise armhf 2.4.1-23 [704 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 303 MB in 34s (8790 kB/s)
Selecting previously unselected package m4.
(Reading database ... 12577 files and directories currently installed.)
Preparing to unpack .../00-m4_1.4.19-4_armhf.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package flex.
Preparing to unpack .../01-flex_2.6.4-8.2_armhf.deb ...
Unpacking flex (2.6.4-8.2) ...
Selecting previously unselected package libfftw3-double3:armhf.
Preparing to unpack .../02-libfftw3-double3_3.3.10-1_armhf.deb ...
Unpacking libfftw3-double3:armhf (3.3.10-1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../03-libexpat1_2.5.0-2_armhf.deb ...
Unpacking libexpat1:armhf (2.5.0-2) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../04-libbrotli1_1.0.9-2+b3_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b3) ...
Selecting previously unselected package libpng16-16:armhf.
Preparing to unpack .../05-libpng16-16_1.6.40-2_armhf.deb ...
Unpacking libpng16-16:armhf (1.6.40-2) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../06-libfreetype6_2.13.2+dfsg-1_armhf.deb ...
Unpacking libfreetype6:armhf (2.13.2+dfsg-1) ...
Selecting previously unselected package fonts-dejavu-mono.
Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ...
Unpacking fonts-dejavu-mono (2.37-8) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../08-fonts-dejavu-core_2.37-8_all.deb ...
Unpacking fonts-dejavu-core (2.37-8) ...
Selecting previously unselected package libfontenc1:armhf.
Preparing to unpack .../09-libfontenc1_1%3a1.1.4-1_armhf.deb ...
Unpacking libfontenc1:armhf (1:1.1.4-1) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../10-x11-common_1%3a7.7+23_all.deb ...
Unpacking x11-common (1:7.7+23) ...
Selecting previously unselected package xfonts-encodings.
Preparing to unpack .../11-xfonts-encodings_1%3a1.0.4-2.2_all.deb ...
Unpacking xfonts-encodings (1:1.0.4-2.2) ...
Selecting previously unselected package xfonts-utils.
Preparing to unpack .../12-xfonts-utils_1%3a7.7+6_armhf.deb ...
Unpacking xfonts-utils (1:7.7+6) ...
Selecting previously unselected package fonts-urw-base35.
Preparing to unpack .../13-fonts-urw-base35_20200910-7_all.deb ...
Unpacking fonts-urw-base35 (20200910-7) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../14-fontconfig-config_2.14.2-6_armhf.deb ...
Unpacking fontconfig-config (2.14.2-6) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../15-libfontconfig1_2.14.2-6_armhf.deb ...
Unpacking libfontconfig1:armhf (2.14.2-6) ...
Selecting previously unselected package libsharpyuv0:armhf.
Preparing to unpack .../16-libsharpyuv0_1.3.2-0.3_armhf.deb ...
Unpacking libsharpyuv0:armhf (1.3.2-0.3) ...
Selecting previously unselected package libdav1d6:armhf.
Preparing to unpack .../17-libdav1d6_1.2.1-2+rpi1_armhf.deb ...
Unpacking libdav1d6:armhf (1.2.1-2+rpi1) ...
Selecting previously unselected package libheif-plugin-dav1d:armhf.
Preparing to unpack .../18-libheif-plugin-dav1d_1.17.1-1_armhf.deb ...
Unpacking libheif-plugin-dav1d:armhf (1.17.1-1) ...
Selecting previously unselected package libde265-0:armhf.
Preparing to unpack .../19-libde265-0_1.0.11-1+rpi1+b1_armhf.deb ...
Unpacking libde265-0:armhf (1.0.11-1+rpi1+b1) ...
Selecting previously unselected package libheif-plugin-libde265:armhf.
Preparing to unpack .../20-libheif-plugin-libde265_1.17.1-1_armhf.deb ...
Unpacking libheif-plugin-libde265:armhf (1.17.1-1) ...
Selecting previously unselected package libheif1:armhf.
Preparing to unpack .../21-libheif1_1.17.1-1_armhf.deb ...
Unpacking libheif1:armhf (1.17.1-1) ...
Selecting previously unselected package libjbig0:armhf.
Preparing to unpack .../22-libjbig0_2.1-6.1_armhf.deb ...
Unpacking libjbig0:armhf (2.1-6.1) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../23-libjpeg62-turbo_1%3a2.1.5-2_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.1.5-2) ...
Selecting previously unselected package liblcms2-2:armhf.
Preparing to unpack .../24-liblcms2-2_2.14-2_armhf.deb ...
Unpacking liblcms2-2:armhf (2.14-2) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../25-libglib2.0-0_2.78.1-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.78.1-2) ...
Selecting previously unselected package liblqr-1-0:armhf.
Preparing to unpack .../26-liblqr-1-0_0.4.2-2.1_armhf.deb ...
Unpacking liblqr-1-0:armhf (0.4.2-2.1) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../27-libltdl7_2.4.7-7_armhf.deb ...
Unpacking libltdl7:armhf (2.4.7-7) ...
Selecting previously unselected package libopenjp2-7:armhf.
Preparing to unpack .../28-libopenjp2-7_2.5.0-2_armhf.deb ...
Unpacking libopenjp2-7:armhf (2.5.0-2) ...
Selecting previously unselected package libraw23:armhf.
Preparing to unpack .../29-libraw23_0.21.1-7+rpi1_armhf.deb ...
Unpacking libraw23:armhf (0.21.1-7+rpi1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../30-libdeflate0_1.18-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.18-1) ...
Selecting previously unselected package liblerc4:armhf.
Preparing to unpack .../31-liblerc4_4.0.0+ds-3_armhf.deb ...
Unpacking liblerc4:armhf (4.0.0+ds-3) ...
Selecting previously unselected package libwebp7:armhf.
Preparing to unpack .../32-libwebp7_1.3.2-0.3_armhf.deb ...
Unpacking libwebp7:armhf (1.3.2-0.3) ...
Selecting previously unselected package libtiff6:armhf.
Preparing to unpack .../33-libtiff6_4.5.1+git230720-1_armhf.deb ...
Unpacking libtiff6:armhf (4.5.1+git230720-1) ...
Selecting previously unselected package libwebpdemux2:armhf.
Preparing to unpack .../34-libwebpdemux2_1.3.2-0.3_armhf.deb ...
Unpacking libwebpdemux2:armhf (1.3.2-0.3) ...
Selecting previously unselected package libwebpmux3:armhf.
Preparing to unpack .../35-libwebpmux3_1.3.2-0.3_armhf.deb ...
Unpacking libwebpmux3:armhf (1.3.2-0.3) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../36-libxau6_1%3a1.0.9-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.9-1) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../37-libbsd0_0.11.7-4_armhf.deb ...
Unpacking libbsd0:armhf (0.11.7-4) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../38-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../39-libxcb1_1.15-1_armhf.deb ...
Unpacking libxcb1:armhf (1.15-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../40-libx11-data_2%3a1.8.7-1_all.deb ...
Unpacking libx11-data (2:1.8.7-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../41-libx11-6_2%3a1.8.7-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.8.7-1) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../42-libxext6_2%3a1.3.4-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.4-1) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../43-libicu72_72.1-4_armhf.deb ...
Unpacking libicu72:armhf (72.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../44-libxml2_2.9.14+dfsg-1.3_armhf.deb ...
Unpacking libxml2:armhf (2.9.14+dfsg-1.3) ...
Selecting previously unselected package imagemagick-6-common.
Preparing to unpack .../45-imagemagick-6-common_8%3a6.9.12.98+dfsg1-3_all.deb ...
Unpacking imagemagick-6-common (8:6.9.12.98+dfsg1-3) ...
Selecting previously unselected package libmagickcore-6.q16-7:armhf.
Preparing to unpack .../46-libmagickcore-6.q16-7_8%3a6.9.12.98+dfsg1-3_armhf.deb ...
Unpacking libmagickcore-6.q16-7:armhf (8:6.9.12.98+dfsg1-3) ...
Selecting previously unselected package libmagickwand-6.q16-7:armhf.
Preparing to unpack .../47-libmagickwand-6.q16-7_8%3a6.9.12.98+dfsg1-3_armhf.deb ...
Unpacking libmagickwand-6.q16-7:armhf (8:6.9.12.98+dfsg1-3) ...
Selecting previously unselected package poppler-data.
Preparing to unpack .../48-poppler-data_0.4.12-1_all.deb ...
Unpacking poppler-data (0.4.12-1) ...
Selecting previously unselected package libpython3.11-minimal:armhf.
Preparing to unpack .../49-libpython3.11-minimal_3.11.6-3_armhf.deb ...
Unpacking libpython3.11-minimal:armhf (3.11.6-3) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../50-python3.11-minimal_3.11.6-3_armhf.deb ...
Unpacking python3.11-minimal (3.11.6-3) ...
Setting up libpython3.11-minimal:armhf (3.11.6-3) ...
Setting up libexpat1:armhf (2.5.0-2) ...
Setting up python3.11-minimal (3.11.6-3) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 14859 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.11.4-5_armhf.deb ...
Unpacking python3-minimal (3.11.4-5) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package mailcap.
Preparing to unpack .../2-mailcap_3.70+nmu1_all.deb ...
Unpacking mailcap (3.70+nmu1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../3-mime-support_3.66_all.deb ...
Unpacking mime-support (3.66) ...
Selecting previously unselected package libpython3.11-stdlib:armhf.
Preparing to unpack .../4-libpython3.11-stdlib_3.11.6-3_armhf.deb ...
Unpacking libpython3.11-stdlib:armhf (3.11.6-3) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../5-python3.11_3.11.6-3_armhf.deb ...
Unpacking python3.11 (3.11.6-3) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../6-libpython3-stdlib_3.11.4-5_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.11.4-5) ...
Setting up python3-minimal (3.11.4-5) ...
Selecting previously unselected package python3.
(Reading database ... 15299 files and directories currently installed.)
Preparing to unpack .../000-python3_3.11.4-5_armhf.deb ...
Unpacking python3 (3.11.4-5) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../001-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../002-groff-base_1.23.0-3_armhf.deb ...
Unpacking groff-base (1.23.0-3) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../003-bsdextrautils_2.39.2-5_armhf.deb ...
Unpacking bsdextrautils (2.39.2-5) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../004-libpipeline1_1.5.7-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../005-man-db_2.12.0-1_armhf.deb ...
Unpacking man-db (2.12.0-1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../006-sensible-utils_0.0.20_all.deb ...
Unpacking sensible-utils (0.0.20) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../007-libmagic-mgc_1%3a5.45-2_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../008-libmagic1_1%3a5.45-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.45-2) ...
Selecting previously unselected package file.
Preparing to unpack .../009-file_1%3a5.45-2_armhf.deb ...
Unpacking file (1:5.45-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../010-gettext-base_0.21-13_armhf.deb ...
Unpacking gettext-base (0.21-13) ...
Selecting previously unselected package ucf.
Preparing to unpack .../011-ucf_3.0043+nmu1_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043+nmu1) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../012-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../013-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../014-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../015-autopoint_0.21-13_all.deb ...
Unpacking autopoint (0.21-13) ...
Selecting previously unselected package libtcl8.6:armhf.
Preparing to unpack .../016-libtcl8.6_8.6.13+dfsg-2_armhf.deb ...
Unpacking libtcl8.6:armhf (8.6.13+dfsg-2) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../017-libxrender1_1%3a0.9.10-1.1_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1.1) ...
Selecting previously unselected package libxft2:armhf.
Preparing to unpack .../018-libxft2_2.3.6-1_armhf.deb ...
Unpacking libxft2:armhf (2.3.6-1) ...
Selecting previously unselected package libxss1:armhf.
Preparing to unpack .../019-libxss1_1%3a1.2.3-1_armhf.deb ...
Unpacking libxss1:armhf (1:1.2.3-1) ...
Selecting previously unselected package libtk8.6:armhf.
Preparing to unpack .../020-libtk8.6_8.6.13-2_armhf.deb ...
Unpacking libtk8.6:armhf (8.6.13-2) ...
Selecting previously unselected package tk8.6-blt2.5.
Preparing to unpack .../021-tk8.6-blt2.5_2.5.3+dfsg-4.1_armhf.deb ...
Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Selecting previously unselected package blt.
Preparing to unpack .../022-blt_2.5.3+dfsg-4.1_armhf.deb ...
Unpacking blt (2.5.3+dfsg-4.1) ...
Selecting previously unselected package bwa.
Preparing to unpack .../023-bwa_0.7.17-7_armhf.deb ...
Unpacking bwa (0.7.17-7) ...
Selecting previously unselected package libargtable2-0.
Preparing to unpack .../024-libargtable2-0_13-1.1_armhf.deb ...
Unpacking libargtable2-0 (13-1.1) ...
Selecting previously unselected package clustalo.
Preparing to unpack .../025-clustalo_1.2.4-7_armhf.deb ...
Unpacking clustalo (1.2.4-7) ...
Selecting previously unselected package clustalw.
Preparing to unpack .../026-clustalw_2.1+lgpl-7_armhf.deb ...
Unpacking clustalw (2.1+lgpl-7) ...
Preparing to unpack .../027-dpkg-dev_1.22.1+rpi1_all.deb ...
Unpacking dpkg-dev (1.22.1+rpi1) over (1.22.0+rpi1) ...
Preparing to unpack .../028-libdpkg-perl_1.22.1+rpi1_all.deb ...
Unpacking libdpkg-perl (1.22.1+rpi1) over (1.22.0+rpi1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../029-libdebhelper-perl_13.11.7_all.deb ...
Unpacking libdebhelper-perl (13.11.7) ...
Selecting previously unselected package libtool.
Preparing to unpack .../030-libtool_2.4.7-7_all.deb ...
Unpacking libtool (2.4.7-7) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../031-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../032-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../033-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../034-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../035-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../036-libelf1_0.188-2.1+rpi1_armhf.deb ...
Unpacking libelf1:armhf (0.188-2.1+rpi1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../037-dwz_0.15-1_armhf.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../038-gettext_0.21-13_armhf.deb ...
Unpacking gettext (0.21-13) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../039-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../040-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../041-debhelper_13.11.7_all.deb ...
Unpacking debhelper (13.11.7) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../042-python3-lib2to3_3.11.5-1_all.deb ...
Unpacking python3-lib2to3 (3.11.5-1) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../043-python3-distutils_3.11.5-1_all.deb ...
Unpacking python3-distutils (3.11.5-1) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../044-python3-pkg-resources_68.1.2-2_all.deb ...
Unpacking python3-pkg-resources (68.1.2-2) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../045-python3-setuptools_68.1.2-2_all.deb ...
Unpacking python3-setuptools (68.1.2-2) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../046-dh-python_6.20231107_all.deb ...
Unpacking dh-python (6.20231107) ...
Selecting previously unselected package dialign.
Preparing to unpack .../047-dialign_2.2.1-11_armhf.deb ...
Unpacking dialign (2.2.1-11) ...
Selecting previously unselected package libboost-regex1.74.0:armhf.
Preparing to unpack .../048-libboost-regex1.74.0_1.74.0+ds1-23_armhf.deb ...
Unpacking libboost-regex1.74.0:armhf (1.74.0+ds1-23) ...
Selecting previously unselected package libcifpp-data.
Preparing to unpack .../049-libcifpp-data_5.0.7.1-3_all.deb ...
Unpacking libcifpp-data (5.0.7.1-3) ...
Selecting previously unselected package libcifpp5:armhf.
Preparing to unpack .../050-libcifpp5_5.0.7.1-3_armhf.deb ...
Unpacking libcifpp5:armhf (5.0.7.1-3) ...
Selecting previously unselected package dssp.
Preparing to unpack .../051-dssp_4.2.2-2_armhf.deb ...
Unpacking dssp (4.2.2-2) ...
Selecting previously unselected package libaom3:armhf.
Preparing to unpack .../052-libaom3_3.7.0-1_armhf.deb ...
Unpacking libaom3:armhf (3.7.0-1) ...
Selecting previously unselected package libabsl20220623:armhf.
Preparing to unpack .../053-libabsl20220623_20220623.1-3_armhf.deb ...
Unpacking libabsl20220623:armhf (20220623.1-3) ...
Selecting previously unselected package libgav1-1:armhf.
Preparing to unpack .../054-libgav1-1_0.18.0-1+rpi1+b1_armhf.deb ...
Unpacking libgav1-1:armhf (0.18.0-1+rpi1+b1) ...
Selecting previously unselected package librav1e0:armhf.
Preparing to unpack .../055-librav1e0_0.6.6-3+rpi1_armhf.deb ...
Unpacking librav1e0:armhf (0.6.6-3+rpi1) ...
Selecting previously unselected package libsvtav1enc1d1:armhf.
Preparing to unpack .../056-libsvtav1enc1d1_1.7.0+dfsg-2_armhf.deb ...
Unpacking libsvtav1enc1d1:armhf (1.7.0+dfsg-2) ...
Selecting previously unselected package libyuv0:armhf.
Preparing to unpack .../057-libyuv0_0.0~git20230907.cbfb661-1_armhf.deb ...
Unpacking libyuv0:armhf (0.0~git20230907.cbfb661-1) ...
Selecting previously unselected package libavif16:armhf.
Preparing to unpack .../058-libavif16_1.0.1-2_armhf.deb ...
Unpacking libavif16:armhf (1.0.1-2) ...
Selecting previously unselected package libxpm4:armhf.
Preparing to unpack .../059-libxpm4_1%3a3.5.17-1_armhf.deb ...
Unpacking libxpm4:armhf (1:3.5.17-1) ...
Selecting previously unselected package libgd3:armhf.
Preparing to unpack .../060-libgd3_2.3.3-9+b1_armhf.deb ...
Unpacking libgd3:armhf (2.3.3-9+b1) ...
Selecting previously unselected package libhpdf-2.3.0:armhf.
Preparing to unpack .../061-libhpdf-2.3.0_2.3.0+dfsg-1_armhf.deb ...
Unpacking libhpdf-2.3.0:armhf (2.3.0+dfsg-1) ...
Selecting previously unselected package mysql-common.
Preparing to unpack .../062-mysql-common_5.8+1.1.0_all.deb ...
Unpacking mysql-common (5.8+1.1.0) ...
Selecting previously unselected package mariadb-common.
Preparing to unpack .../063-mariadb-common_1%3a10.11.3-1+rpi1_all.deb ...
Unpacking mariadb-common (1:10.11.3-1+rpi1) ...
Selecting previously unselected package libmariadb3:armhf.
Preparing to unpack .../064-libmariadb3_1%3a10.11.3-1+rpi1_armhf.deb ...
Unpacking libmariadb3:armhf (1:10.11.3-1+rpi1) ...
Selecting previously unselected package libpq5:armhf.
Preparing to unpack .../065-libpq5_16.0-2_armhf.deb ...
Unpacking libpq5:armhf (16.0-2) ...
Selecting previously unselected package emboss-lib.
Preparing to unpack .../066-emboss-lib_6.6.0+dfsg-12_armhf.deb ...
Unpacking emboss-lib (6.6.0+dfsg-12) ...
Selecting previously unselected package emboss-data.
Preparing to unpack .../067-emboss-data_6.6.0+dfsg-12_all.deb ...
Unpacking emboss-data (6.6.0+dfsg-12) ...
Selecting previously unselected package emboss.
Preparing to unpack .../068-emboss_6.6.0+dfsg-12_armhf.deb ...
Unpacking emboss (6.6.0+dfsg-12) ...
Selecting previously unselected package fasttree.
Preparing to unpack .../069-fasttree_2.1.11-2_armhf.deb ...
Unpacking fasttree (2.1.11-2) ...
Selecting previously unselected package fonts-dejavu-extra.
Preparing to unpack .../070-fonts-dejavu-extra_2.37-8_all.deb ...
Unpacking fonts-dejavu-extra (2.37-8) ...
Selecting previously unselected package fonts-lmodern.
Preparing to unpack .../071-fonts-lmodern_2.005-1_all.deb ...
Unpacking fonts-lmodern (2.005-1) ...
Selecting previously unselected package fonts-lyx.
Preparing to unpack .../072-fonts-lyx_2.3.7-1_all.deb ...
Unpacking fonts-lyx (2.3.7-1) ...
Selecting previously unselected package libgs-common.
Preparing to unpack .../073-libgs-common_10.02.0~dfsg-2_all.deb ...
Unpacking libgs-common (10.02.0~dfsg-2) ...
Selecting previously unselected package libgs10-common.
Preparing to unpack .../074-libgs10-common_10.02.0~dfsg-2_all.deb ...
Unpacking libgs10-common (10.02.0~dfsg-2) ...
Selecting previously unselected package libavahi-common-data:armhf.
Preparing to unpack .../075-libavahi-common-data_0.8-13_armhf.deb ...
Unpacking libavahi-common-data:armhf (0.8-13) ...
Selecting previously unselected package libavahi-common3:armhf.
Preparing to unpack .../076-libavahi-common3_0.8-13_armhf.deb ...
Unpacking libavahi-common3:armhf (0.8-13) ...
Selecting previously unselected package libdbus-1-3:armhf.
Preparing to unpack .../077-libdbus-1-3_1.14.10-3_armhf.deb ...
Unpacking libdbus-1-3:armhf (1.14.10-3) ...
Selecting previously unselected package libavahi-client3:armhf.
Preparing to unpack .../078-libavahi-client3_0.8-13_armhf.deb ...
Unpacking libavahi-client3:armhf (0.8-13) ...
Selecting previously unselected package libcups2:armhf.
Preparing to unpack .../079-libcups2_2.4.7-1_armhf.deb ...
Unpacking libcups2:armhf (2.4.7-1) ...
Selecting previously unselected package libidn12:armhf.
Preparing to unpack .../080-libidn12_1.41-1+b1_armhf.deb ...
Unpacking libidn12:armhf (1.41-1+b1) ...
Selecting previously unselected package libijs-0.35:armhf.
Preparing to unpack .../081-libijs-0.35_0.35-15.1_armhf.deb ...
Unpacking libijs-0.35:armhf (0.35-15.1) ...
Selecting previously unselected package libjbig2dec0:armhf.
Preparing to unpack .../082-libjbig2dec0_0.19-3+b2_armhf.deb ...
Unpacking libjbig2dec0:armhf (0.19-3+b2) ...
Selecting previously unselected package libpaper1:armhf.
Preparing to unpack .../083-libpaper1_1.1.29_armhf.deb ...
Unpacking libpaper1:armhf (1.1.29) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../084-libice6_2%3a1.0.10-1_armhf.deb ...
Unpacking libice6:armhf (2:1.0.10-1) ...
Selecting previously unselected package libsm6:armhf.
Preparing to unpack .../085-libsm6_2%3a1.2.3-1_armhf.deb ...
Unpacking libsm6:armhf (2:1.2.3-1) ...
Selecting previously unselected package libxt6:armhf.
Preparing to unpack .../086-libxt6_1%3a1.2.1-1.1_armhf.deb ...
Unpacking libxt6:armhf (1:1.2.1-1.1) ...
Selecting previously unselected package libgs10:armhf.
Preparing to unpack .../087-libgs10_10.02.0~dfsg-2_armhf.deb ...
Unpacking libgs10:armhf (10.02.0~dfsg-2) ...
Selecting previously unselected package ghostscript.
Preparing to unpack .../088-ghostscript_10.02.0~dfsg-2_armhf.deb ...
Unpacking ghostscript (10.02.0~dfsg-2) ...
Selecting previously unselected package libnetpbm11:armhf.
Preparing to unpack .../089-libnetpbm11_2%3a11.03.06-1_armhf.deb ...
Unpacking libnetpbm11:armhf (2:11.03.06-1) ...
Selecting previously unselected package netpbm.
Preparing to unpack .../090-netpbm_2%3a11.03.06-1_armhf.deb ...
Unpacking netpbm (2:11.03.06-1) ...
Selecting previously unselected package tex-common.
Preparing to unpack .../091-tex-common_6.18_all.deb ...
Unpacking tex-common (6.18) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../092-libpaper-utils_1.1.29_armhf.deb ...
Unpacking libpaper-utils (1.1.29) ...
Selecting previously unselected package libkpathsea6:armhf.
Preparing to unpack .../093-libkpathsea6_2023.20230311.66589-6_armhf.deb ...
Unpacking libkpathsea6:armhf (2023.20230311.66589-6) ...
Selecting previously unselected package libptexenc1:armhf.
Preparing to unpack .../094-libptexenc1_2023.20230311.66589-6_armhf.deb ...
Unpacking libptexenc1:armhf (2023.20230311.66589-6) ...
Selecting previously unselected package libsynctex2:armhf.
Preparing to unpack .../095-libsynctex2_2023.20230311.66589-6_armhf.deb ...
Unpacking libsynctex2:armhf (2023.20230311.66589-6) ...
Selecting previously unselected package libtexlua53-5:armhf.
Preparing to unpack .../096-libtexlua53-5_2023.20230311.66589-6_armhf.deb ...
Unpacking libtexlua53-5:armhf (2023.20230311.66589-6) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../097-t1utils_1.41-4_armhf.deb ...
Unpacking t1utils (1.41-4) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../098-libpixman-1-0_0.42.2-1_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.42.2-1) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../099-libxcb-render0_1.15-1_armhf.deb ...
Unpacking libxcb-render0:armhf (1.15-1) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../100-libxcb-shm0_1.15-1_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.15-1) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../101-libcairo2_1.18.0-1_armhf.deb ...
Unpacking libcairo2:armhf (1.18.0-1) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../102-libgraphite2-3_1.3.14-1_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.14-1) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../103-libharfbuzz0b_8.0.1-1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (8.0.1-1) ...
Selecting previously unselected package libpotrace0:armhf.
Preparing to unpack .../104-libpotrace0_1.16-2_armhf.deb ...
Unpacking libpotrace0:armhf (1.16-2) ...
Selecting previously unselected package libteckit0:armhf.
Preparing to unpack .../105-libteckit0_2.5.11+ds1-1_armhf.deb ...
Unpacking libteckit0:armhf (2.5.11+ds1-1) ...
Selecting previously unselected package libxmu6:armhf.
Preparing to unpack .../106-libxmu6_2%3a1.1.3-3_armhf.deb ...
Unpacking libxmu6:armhf (2:1.1.3-3) ...
Selecting previously unselected package libxaw7:armhf.
Preparing to unpack .../107-libxaw7_2%3a1.0.14-1_armhf.deb ...
Unpacking libxaw7:armhf (2:1.0.14-1) ...
Selecting previously unselected package libxi6:armhf.
Preparing to unpack .../108-libxi6_2%3a1.8-1_armhf.deb ...
Unpacking libxi6:armhf (2:1.8-1) ...
Selecting previously unselected package libzzip-0-13:armhf.
Preparing to unpack .../109-libzzip-0-13_0.13.72+dfsg.1-1.1_armhf.deb ...
Unpacking libzzip-0-13:armhf (0.13.72+dfsg.1-1.1) ...
Selecting previously unselected package texlive-binaries.
Preparing to unpack .../110-texlive-binaries_2023.20230311.66589-6_armhf.deb ...
Unpacking texlive-binaries (2023.20230311.66589-6) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../111-xdg-utils_1.1.3-4.1_all.deb ...
Unpacking xdg-utils (1.1.3-4.1) ...
Selecting previously unselected package texlive-base.
Preparing to unpack .../112-texlive-base_2023.20231007-1_all.deb ...
Unpacking texlive-base (2023.20231007-1) ...
Selecting previously unselected package hicolor-icon-theme.
Preparing to unpack .../113-hicolor-icon-theme_0.17-2_all.deb ...
Unpacking hicolor-icon-theme (0.17-2) ...
Selecting previously unselected package imagemagick-6.q16.
Preparing to unpack .../114-imagemagick-6.q16_8%3a6.9.12.98+dfsg1-3_armhf.deb ...
Unpacking imagemagick-6.q16 (8:6.9.12.98+dfsg1-3) ...
Selecting previously unselected package imagemagick.
Preparing to unpack .../115-imagemagick_8%3a6.9.12.98+dfsg1-3_armhf.deb ...
Unpacking imagemagick (8:6.9.12.98+dfsg1-3) ...
Selecting previously unselected package hevea.
Preparing to unpack .../116-hevea_2.36-2_armhf.deb ...
Unpacking hevea (2.36-2) ...
Selecting previously unselected package libapache-pom-java.
Preparing to unpack .../117-libapache-pom-java_29-2_all.deb ...
Unpacking libapache-pom-java (29-2) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../118-libblas3_3.11.0-2_armhf.deb ...
Unpacking libblas3:armhf (3.11.0-2) ...
Selecting previously unselected package libcommons-parent-java.
Preparing to unpack .../119-libcommons-parent-java_56-1_all.deb ...
Unpacking libcommons-parent-java (56-1) ...
Selecting previously unselected package libcommons-logging-java.
Preparing to unpack .../120-libcommons-logging-java_1.2-4_all.deb ...
Unpacking libcommons-logging-java (1.2-4) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../121-libnghttp2-14_1.58.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.58.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../122-libpsl5_0.21.2-1+b1_armhf.deb ...
Unpacking libpsl5:armhf (0.21.2-1+b1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../123-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../124-libssh2-1_1.11.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.11.0-2) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../125-libcurl3-gnutls_8.4.0-2+rpi1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Selecting previously unselected package libexpat1-dev:armhf.
Preparing to unpack .../126-libexpat1-dev_2.5.0-2_armhf.deb ...
Unpacking libexpat1-dev:armhf (2.5.0-2) ...
Selecting previously unselected package libfontbox-java.
Preparing to unpack .../127-libfontbox-java_1%3a1.8.16-4_all.deb ...
Unpacking libfontbox-java (1:1.8.16-4) ...
Selecting previously unselected package libfribidi0:armhf.
Preparing to unpack .../128-libfribidi0_1.0.13-3_armhf.deb ...
Unpacking libfribidi0:armhf (1.0.13-3) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../129-libgfortran5_13.2.0-5+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (13.2.0-5+rpi1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../130-libhtscodecs2_1.5.2-1_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.5.2-1) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../131-libhts3_1.18+ds-1_armhf.deb ...
Unpacking libhts3:armhf (1.18+ds-1) ...
Selecting previously unselected package libimagequant0:armhf.
Preparing to unpack .../132-libimagequant0_2.17.0-1_armhf.deb ...
Unpacking libimagequant0:armhf (2.17.0-1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../133-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../134-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../135-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Selecting previously unselected package libjs-sphinxdoc.
Preparing to unpack .../136-libjs-sphinxdoc_7.2.6-2_all.deb ...
Unpacking libjs-sphinxdoc (7.2.6-2) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../137-liblapack3_3.11.0-2_armhf.deb ...
Unpacking liblapack3:armhf (3.11.0-2) ...
Selecting previously unselected package liblbfgsb0:armhf.
Preparing to unpack .../138-liblbfgsb0_3.0+dfsg.4-1_armhf.deb ...
Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1) ...
Selecting previously unselected package liblmdb0:armhf.
Preparing to unpack .../139-liblmdb0_0.9.31-1_armhf.deb ...
Unpacking liblmdb0:armhf (0.9.31-1) ...
Selecting previously unselected package libmbedcrypto7:armhf.
Preparing to unpack .../140-libmbedcrypto7_2.28.5-1_armhf.deb ...
Unpacking libmbedcrypto7:armhf (2.28.5-1) ...
Selecting previously unselected package libmbedx509-1:armhf.
Preparing to unpack .../141-libmbedx509-1_2.28.5-1_armhf.deb ...
Unpacking libmbedx509-1:armhf (2.28.5-1) ...
Selecting previously unselected package libmbedtls14:armhf.
Preparing to unpack .../142-libmbedtls14_2.28.5-1_armhf.deb ...
Unpacking libmbedtls14:armhf (2.28.5-1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../143-libncurses6_6.4+20231016-1_armhf.deb ...
Unpacking libncurses6:armhf (6.4+20231016-1) ...
Selecting previously unselected package libpdfbox-java.
Preparing to unpack .../144-libpdfbox-java_1%3a1.8.16-4_all.deb ...
Unpacking libpdfbox-java (1:1.8.16-4) ...
Selecting previously unselected package libpython3.11:armhf.
Preparing to unpack .../145-libpython3.11_3.11.6-3_armhf.deb ...
Unpacking libpython3.11:armhf (3.11.6-3) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../146-zlib1g-dev_1%3a1.2.13.dfsg-3_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Selecting previously unselected package libpython3.11-dev:armhf.
Preparing to unpack .../147-libpython3.11-dev_3.11.6-3_armhf.deb ...
Unpacking libpython3.11-dev:armhf (3.11.6-3) ...
Selecting previously unselected package libpython3-dev:armhf.
Preparing to unpack .../148-libpython3-dev_3.11.4-5_armhf.deb ...
Unpacking libpython3-dev:armhf (3.11.4-5) ...
Selecting previously unselected package libpython3-all-dev:armhf.
Preparing to unpack .../149-libpython3-all-dev_3.11.4-5_armhf.deb ...
Unpacking libpython3-all-dev:armhf (3.11.4-5) ...
Selecting previously unselected package libqhull-r8.0:armhf.
Preparing to unpack .../150-libqhull-r8.0_2020.2-6_armhf.deb ...
Unpacking libqhull-r8.0:armhf (2020.2-6) ...
Selecting previously unselected package libraqm0:armhf.
Preparing to unpack .../151-libraqm0_0.10.1-1_armhf.deb ...
Unpacking libraqm0:armhf (0.10.1-1) ...
Selecting previously unselected package libxslt1.1:armhf.
Preparing to unpack .../152-libxslt1.1_1.1.35-1_armhf.deb ...
Unpacking libxslt1.1:armhf (1.1.35-1) ...
Selecting previously unselected package mafft.
Preparing to unpack .../153-mafft_7.505-1_armhf.deb ...
Unpacking mafft (7.505-1) ...
Selecting previously unselected package ncbi-data.
Preparing to unpack .../154-ncbi-data_6.1.20170106+dfsg1-10_all.deb ...
Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
Selecting previously unselected package ncbi-blast+.
Preparing to unpack .../155-ncbi-blast+_2.12.0+ds-4_armhf.deb ...
Unpacking ncbi-blast+ (2.12.0+ds-4) ...
Selecting previously unselected package phylip.
Preparing to unpack .../156-phylip_1%3a3.697+dfsg-2_armhf.deb ...
Unpacking phylip (1:3.697+dfsg-2) ...
Selecting previously unselected package prank.
Preparing to unpack .../157-prank_0.0.170427+dfsg-3_armhf.deb ...
Unpacking prank (0.0.170427+dfsg-3) ...
Selecting previously unselected package preview-latex-style.
Preparing to unpack .../158-preview-latex-style_12.2-1_all.deb ...
Unpacking preview-latex-style (12.2-1) ...
Selecting previously unselected package probcons.
Preparing to unpack .../159-probcons_1.12-14_armhf.deb ...
Unpacking probcons (1.12-14) ...
Selecting previously unselected package python-matplotlib-data.
Preparing to unpack .../160-python-matplotlib-data_3.6.3-1_all.deb ...
Unpacking python-matplotlib-data (3.6.3-1) ...
Selecting previously unselected package python3-all.
Preparing to unpack .../161-python3-all_3.11.4-5_armhf.deb ...
Unpacking python3-all (3.11.4-5) ...
Selecting previously unselected package python3.11-dev.
Preparing to unpack .../162-python3.11-dev_3.11.6-3_armhf.deb ...
Unpacking python3.11-dev (3.11.6-3) ...
Selecting previously unselected package python3-dev.
Preparing to unpack .../163-python3-dev_3.11.4-5_armhf.deb ...
Unpacking python3-dev (3.11.4-5) ...
Selecting previously unselected package python3-all-dev.
Preparing to unpack .../164-python3-all-dev_3.11.4-5_armhf.deb ...
Unpacking python3-all-dev (3.11.4-5) ...
Selecting previously unselected package python3-appdirs.
Preparing to unpack .../165-python3-appdirs_1.4.4-4_all.deb ...
Unpacking python3-appdirs (1.4.4-4) ...
Selecting previously unselected package python3-attr.
Preparing to unpack .../166-python3-attr_23.1.0-2_all.deb ...
Unpacking python3-attr (23.1.0-2) ...
Selecting previously unselected package python3-brotli.
Preparing to unpack .../167-python3-brotli_1.0.9-2+b3_armhf.deb ...
Unpacking python3-brotli (1.0.9-2+b3) ...
Selecting previously unselected package python3-cairo:armhf.
Preparing to unpack .../168-python3-cairo_1.24.0-3_armhf.deb ...
Unpacking python3-cairo:armhf (1.24.0-3) ...
Selecting previously unselected package python3-numpy.
Preparing to unpack .../169-python3-numpy_1%3a1.24.2-1_armhf.deb ...
Unpacking python3-numpy (1:1.24.2-1) ...
Selecting previously unselected package python3-contourpy.
Preparing to unpack .../170-python3-contourpy_1.0.7-1_armhf.deb ...
Unpacking python3-contourpy (1.0.7-1) ...
Selecting previously unselected package python3-cycler.
Preparing to unpack .../171-python3-cycler_0.11.0-1_all.deb ...
Unpacking python3-cycler (0.11.0-1) ...
Selecting previously unselected package python3-six.
Preparing to unpack .../172-python3-six_1.16.0-4_all.deb ...
Unpacking python3-six (1.16.0-4) ...
Selecting previously unselected package python3-dateutil.
Preparing to unpack .../173-python3-dateutil_2.8.2-3_all.deb ...
Unpacking python3-dateutil (2.8.2-3) ...
Selecting previously unselected package python3-decorator.
Preparing to unpack .../174-python3-decorator_5.1.1-5_all.deb ...
Unpacking python3-decorator (5.1.1-5) ...
Selecting previously unselected package python3-scipy.
Preparing to unpack .../175-python3-scipy_1.10.1-2+rpi1_armhf.deb ...
Unpacking python3-scipy (1.10.1-2+rpi1) ...
Selecting previously unselected package python3-ufolib2.
Preparing to unpack .../176-python3-ufolib2_0.16.0+dfsg1-1_all.deb ...
Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ...
Selecting previously unselected package python3-mpmath.
Preparing to unpack .../177-python3-mpmath_1.2.1-2_all.deb ...
Unpacking python3-mpmath (1.2.1-2) ...
Selecting previously unselected package python3-sympy.
Preparing to unpack .../178-python3-sympy_1.12-6_all.deb ...
Unpacking python3-sympy (1.12-6) ...
Selecting previously unselected package python3-tz.
Preparing to unpack .../179-python3-tz_2023.3.post1-1_all.deb ...
Unpacking python3-tz (2023.3.post1-1) ...
Selecting previously unselected package python3-fs.
Preparing to unpack .../180-python3-fs_2.4.16-2_all.deb ...
Unpacking python3-fs (2.4.16-2) ...
Selecting previously unselected package python3-lxml:armhf.
Preparing to unpack .../181-python3-lxml_4.9.3-1_armhf.deb ...
Unpacking python3-lxml:armhf (4.9.3-1) ...
Selecting previously unselected package python3-lz4.
Preparing to unpack .../182-python3-lz4_4.0.2+dfsg-1+b1_armhf.deb ...
Unpacking python3-lz4 (4.0.2+dfsg-1+b1) ...
Selecting previously unselected package unicode-data.
Preparing to unpack .../183-unicode-data_15.1.0-1_all.deb ...
Unpacking unicode-data (15.1.0-1) ...
Selecting previously unselected package python3-fonttools.
Preparing to unpack .../184-python3-fonttools_4.38.0-1_armhf.deb ...
Unpacking python3-fonttools (4.38.0-1) ...
Selecting previously unselected package python3-freetype.
Preparing to unpack .../185-python3-freetype_2.4.0-1_all.deb ...
Unpacking python3-freetype (2.4.0-1) ...
Selecting previously unselected package python3-isodate.
Preparing to unpack .../186-python3-isodate_0.6.1-1_all.deb ...
Unpacking python3-isodate (0.6.1-1) ...
Selecting previously unselected package python3-kiwisolver.
Preparing to unpack .../187-python3-kiwisolver_1.4.4-1_armhf.deb ...
Unpacking python3-kiwisolver (1.4.4-1) ...
Selecting previously unselected package python3-pil:armhf.
Preparing to unpack .../188-python3-pil_10.0.0-1_armhf.deb ...
Unpacking python3-pil:armhf (10.0.0-1) ...
Selecting previously unselected package python3-tk:armhf.
Preparing to unpack .../189-python3-tk_3.11.5-1_armhf.deb ...
Unpacking python3-tk:armhf (3.11.5-1) ...
Selecting previously unselected package python3-pil.imagetk:armhf.
Preparing to unpack .../190-python3-pil.imagetk_10.0.0-1_armhf.deb ...
Unpacking python3-pil.imagetk:armhf (10.0.0-1) ...
Selecting previously unselected package python3-pyparsing.
Preparing to unpack .../191-python3-pyparsing_3.1.1-1_all.deb ...
Unpacking python3-pyparsing (3.1.1-1) ...
Selecting previously unselected package python3-packaging.
Preparing to unpack .../192-python3-packaging_23.1-1_all.deb ...
Unpacking python3-packaging (23.1-1) ...
Selecting previously unselected package python3-matplotlib.
Preparing to unpack .../193-python3-matplotlib_3.6.3-1_armhf.deb ...
Unpacking python3-matplotlib (3.6.3-1) ...
Selecting previously unselected package python3-msgpack.
Preparing to unpack .../194-python3-msgpack_1.0.3-3_armhf.deb ...
Unpacking python3-msgpack (1.0.3-3) ...
Selecting previously unselected package python3-mmtf.
Preparing to unpack .../195-python3-mmtf_1.1.3-1_all.deb ...
Unpacking python3-mmtf (1.1.3-1) ...
Selecting previously unselected package python3-mysqldb.
Preparing to unpack .../196-python3-mysqldb_1.4.6-2+b1_armhf.deb ...
Unpacking python3-mysqldb (1.4.6-2+b1) ...
Selecting previously unselected package python3-networkx.
Preparing to unpack .../197-python3-networkx_2.8.8-1_all.deb ...
Unpacking python3-networkx (2.8.8-1) ...
Selecting previously unselected package python3-psycopg2.
Preparing to unpack .../198-python3-psycopg2_2.9.6-3_armhf.deb ...
Unpacking python3-psycopg2 (2.9.6-3) ...
Selecting previously unselected package python3-pygments.
Preparing to unpack .../199-python3-pygments_2.15.1+dfsg-1_all.deb ...
Unpacking python3-pygments (2.15.1+dfsg-1) ...
Selecting previously unselected package python3-rdflib.
Preparing to unpack .../200-python3-rdflib_6.1.1-2_all.deb ...
Unpacking python3-rdflib (6.1.1-2) ...
Selecting previously unselected package python3-rlpycairo.
Preparing to unpack .../201-python3-rlpycairo_0.3.0-3_all.deb ...
Unpacking python3-rlpycairo (0.3.0-3) ...
Selecting previously unselected package python3-reportlab.
Preparing to unpack .../202-python3-reportlab_4.0.4-11_all.deb ...
Unpacking python3-reportlab (4.0.4-11) ...
Selecting previously unselected package python3-unittest2.
Preparing to unpack .../203-python3-unittest2_1.1.0-9_all.deb ...
Unpacking python3-unittest2 (1.1.0-9) ...
Selecting previously unselected package samtools.
Preparing to unpack .../204-samtools_1.18-1_armhf.deb ...
Unpacking samtools (1.18-1) ...
Selecting previously unselected package t-coffee.
Preparing to unpack .../205-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.deb ...
Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ...
Selecting previously unselected package texlive-fonts-recommended.
Preparing to unpack .../206-texlive-fonts-recommended_2023.20231007-1_all.deb ...
Unpacking texlive-fonts-recommended (2023.20231007-1) ...
Selecting previously unselected package texlive-latex-base.
Preparing to unpack .../207-texlive-latex-base_2023.20231007-1_all.deb ...
Unpacking texlive-latex-base (2023.20231007-1) ...
Selecting previously unselected package texlive-latex-recommended.
Preparing to unpack .../208-texlive-latex-recommended_2023.20231007-1_all.deb ...
Unpacking texlive-latex-recommended (2023.20231007-1) ...
Selecting previously unselected package texlive-pictures.
Preparing to unpack .../209-texlive-pictures_2023.20231007-1_all.deb ...
Unpacking texlive-pictures (2023.20231007-1) ...
Selecting previously unselected package texlive-latex-extra.
Preparing to unpack .../210-texlive-latex-extra_2023.20231007-2_all.deb ...
Unpacking texlive-latex-extra (2023.20231007-2) ...
Selecting previously unselected package wise-data.
Preparing to unpack .../211-wise-data_2.4.1-23_all.deb ...
Unpacking wise-data (2.4.1-23) ...
Selecting previously unselected package wise.
Preparing to unpack .../212-wise_2.4.1-23_armhf.deb ...
Unpacking wise (2.4.1-23) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../213-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.5.2-1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up liblmdb0:armhf (0.9.31-1) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up liblcms2-2:armhf (2.14-2) ...
Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
Setting up libpixman-1-0:armhf (0.42.2-1) ...
Setting up libsharpyuv0:armhf (1.3.2-0.3) ...
Setting up libaom3:armhf (3.7.0-1) ...
Setting up mysql-common (5.8+1.1.0) ...
update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libabsl20220623:armhf (20220623.1-3) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up imagemagick-6-common (8:6.9.12.98+dfsg1-3) ...
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up liblerc4:armhf (4.0.0+ds-3) ...
Setting up bsdextrautils (2.39.2-5) ...
Setting up hicolor-icon-theme (0.17-2) ...
Setting up probcons (1.12-14) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up mafft (7.505-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.78.1-2) ...
No schema files found: doing nothing.
Setting up bwa (0.7.17-7) ...
Setting up fonts-lyx (2.3.7-1) ...
Setting up libijs-0.35:armhf (0.35-15.1) ...
Setting up libpython3.11-stdlib:armhf (3.11.6-3) ...
Setting up libdebhelper-perl (13.11.7) ...
Setting up libgs-common (10.02.0~dfsg-2) ...
Setting up libbrotli1:armhf (1.0.9-2+b3) ...
Setting up libfontbox-java (1:1.8.16-4) ...
Setting up phylip (1:3.697+dfsg-2) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up libnghttp2-14:armhf (1.58.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libpq5:armhf (16.0-2) ...
Setting up libnetpbm11:armhf (2:11.03.06-1) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-13) ...
Setting up m4 (1.4.19-4) ...
Setting up libqhull-r8.0:armhf (2020.2-6) ...
Setting up libsvtav1enc1d1:armhf (1.7.0+dfsg-2) ...
Setting up libzzip-0-13:armhf (0.13.72+dfsg.1-1.1) ...
Setting up file (1:5.45-2) ...
Setting up emboss-data (6.6.0+dfsg-12) ...
Setting up libjbig0:armhf (2.1-6.1) ...
Setting up librav1e0:armhf (0.6.6-3+rpi1) ...
Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ...
Setting up poppler-data (0.4.12-1) ...
Setting up unicode-data (15.1.0-1) ...
Setting up mariadb-common (1:10.11.3-1+rpi1) ...
update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libfontenc1:armhf (1:1.1.4-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libexpat1-dev:armhf (2.5.0-2) ...
Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ...
Setting up libmbedcrypto7:armhf (2.28.5-1) ...
Setting up libx11-data (2:1.8.7-1) ...
Setting up libjbig2dec0:armhf (0.19-3+b2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libteckit0:armhf (2.5.11+ds1-1) ...
Setting up libapache-pom-java (29-2) ...
Setting up libavahi-common-data:armhf (0.8-13) ...
Setting up libncurses6:armhf (6.4+20231016-1) ...
Setting up libdbus-1-3:armhf (1.14.10-3) ...
Setting up xfonts-encodings (1:1.0.4-2.2) ...
Setting up libfribidi0:armhf (1.0.13-3) ...
Setting up libboost-regex1.74.0:armhf (1.74.0+ds1-23) ...
Setting up t1utils (1.41-4) ...
Setting up libtexlua53-5:armhf (2023.20230311.66589-6) ...
Setting up libimagequant0:armhf (2.17.0-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16:armhf (1.6.40-2) ...
Setting up libidn12:armhf (1.41-1+b1) ...
Setting up libtcl8.6:armhf (8.6.13+dfsg-2) ...
Setting up autopoint (0.21-13) ...
Setting up libmariadb3:armhf (1:10.11.3-1+rpi1) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libgav1-1:armhf (0.18.0-1+rpi1+b1) ...
Setting up wise-data (2.4.1-23) ...
Setting up libdav1d6:armhf (1.2.1-2+rpi1) ...
Setting up libltdl7:armhf (2.4.7-7) ...
Setting up libfftw3-double3:armhf (3.3.10-1) ...
Setting up libcifpp-data (5.0.7.1-3) ...
Setting up libdpkg-perl (1.22.1+rpi1) ...
Setting up libkpathsea6:armhf (2023.20230311.66589-6) ...
Setting up libgfortran5:armhf (13.2.0-5+rpi1) ...
Setting up autoconf (2.71-3) ...
Setting up libwebp7:armhf (1.3.2-0.3) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Setting up fonts-dejavu-extra (2.37-8) ...
Setting up mount (2.39.2-5) ...
Setting up liblqr-1-0:armhf (0.4.2-2.1) ...
Setting up sensible-utils (0.0.20) ...
Setting up libtiff6:armhf (4.5.1+git230720-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up clustalw (2.1+lgpl-7) ...
Setting up fonts-lmodern (2.005-1) ...
Setting up libopenjp2-7:armhf (2.5.0-2) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:armhf (1.11.0-2) ...
Setting up fasttree (2.1.11-2) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libraw23:armhf (0.21.1-7+rpi1) ...
Setting up libde265-0:armhf (1.0.11-1+rpi1+b1) ...
Setting up python-matplotlib-data (3.6.3-1) ...
Setting up libwebpmux3:armhf (1.3.2-0.3) ...
Setting up libbsd0:armhf (0.11.7-4) ...
Setting up libyuv0:armhf (0.0~git20230907.cbfb661-1) ...
Setting up mailcap (3.70+nmu1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up dialign (2.2.1-11) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up xdg-utils (1.1.3-4.1) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libsynctex2:armhf (2023.20230311.66589-6) ...
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up prank (0.0.170427+dfsg-3) ...
Setting up libargtable2-0 (13-1.1) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up libpotrace0:armhf (1.16-2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up python3.11 (3.11.6-3) ...
Setting up libice6:armhf (2:1.0.10-1) ...
Setting up libavif16:armhf (1.0.1-2) ...
Setting up libhpdf-2.3.0:armhf (2.3.0+dfsg-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up flex (2.6.4-8.2) ...
Setting up liblapack3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-13) ...
Setting up libpdfbox-java (1:1.8.16-4) ...
Setting up mime-support (3.66) ...
Setting up libpython3.11:armhf (3.11.6-3) ...
Setting up libmbedx509-1:armhf (2.28.5-1) ...
Setting up libmbedtls14:armhf (2.28.5-1) ...
Setting up libtool (2.4.7-7) ...
Setting up libxcb-render0:armhf (1.15-1) ...
Setting up fontconfig-config (2.14.2-6) ...
Setting up wise (2.4.1-23) ...
Setting up libwebpdemux2:armhf (1.3.2-0.3) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:armhf (0.8-13) ...
Setting up libcommons-logging-java (1.2-4) ...
Setting up libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Setting up python3 (3.11.4-5) ...
Setting up libxcb-shm0:armhf (1.15-1) ...
Setting up clustalo (1.2.4-7) ...
Setting up python3-tz (2023.3.post1-1) ...
Setting up dpkg-dev (1.22.1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up ncbi-blast+ (2.12.0+ds-4) ...
Setting up libcifpp5:armhf (5.0.7.1-3) ...
Setting up python3-mysqldb (1.4.6-2+b1) ...
Setting up python3-six (1.16.0-4) ...
Setting up dh-autoreconf (20) ...
Setting up python3-isodate (0.6.1-1) ...
Setting up python3-decorator (5.1.1-5) ...
Setting up python3-packaging (23.1-1) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libptexenc1:armhf (2023.20230311.66589-6) ...
Setting up python3-pyparsing (3.1.1-1) ...
Setting up libfreetype6:armhf (2.13.2+dfsg-1) ...
Setting up libpython3.11-dev:armhf (3.11.6-3) ...
Setting up python3-brotli (1.0.9-2+b3) ...
Setting up python3-cycler (0.11.0-1) ...
Setting up python3-kiwisolver (1.4.4-1) ...
Setting up python3-psycopg2 (2.9.6-3) ...
Setting up ucf (3.0043+nmu1) ...
Setting up libjs-sphinxdoc (7.2.6-2) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libxslt1.1:armhf (1.1.35-1) ...
Setting up libx11-6:armhf (2:1.8.7-1) ...
Setting up libharfbuzz0b:armhf (8.0.1-1) ...
Setting up python3-dateutil (2.8.2-3) ...
Setting up python3-msgpack (1.0.3-3) ...
Setting up libfontconfig1:armhf (2.14.2-6) ...
Setting up python3-mpmath (1.2.1-2) ...
Setting up python3-lib2to3 (3.11.5-1) ...
Setting up python3-appdirs (1.4.4-4) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libavahi-client3:armhf (0.8-13) ...
Setting up liblbfgsb0:armhf (3.0+dfsg.4-1) ...
Setting up python3-pkg-resources (68.1.2-2) ...
Setting up python3-distutils (3.11.5-1) ...
Setting up python3-sympy (1.12-6) ...
Setting up python3-attr (23.1.0-2) ...
Setting up libpaper1:armhf (1.1.29) ...

Creating config file /etc/papersize with new version
Setting up libhts3:armhf (1.18+ds-1) ...
Setting up libpython3-dev:armhf (3.11.4-5) ...
Setting up python3-setuptools (68.1.2-2) ...
Setting up libxpm4:armhf (1:3.5.17-1) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up python3-lz4 (4.0.2+dfsg-1+b1) ...
Setting up python3.11-dev (3.11.6-3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up python3-all (3.11.4-5) ...
Setting up libpaper-utils (1.1.29) ...
Setting up dssp (4.2.2-2) ...
Setting up python3-freetype (2.4.0-1) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up python3-networkx (2.8.8-1) ...
Setting up man-db (2.12.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:armhf (1.18.0-1) ...
Setting up samtools (1.18-1) ...
Setting up python3-fs (2.4.16-2) ...
Setting up tex-common (6.18) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up python3-pygments (2.15.1+dfsg-1) ...
Setting up libpython3-all-dev:armhf (3.11.4-5) ...
Setting up libraqm0:armhf (0.10.1-1) ...
Setting up python3-dev (3.11.4-5) ...
Setting up python3-unittest2 (1.1.0-9) ...
update-alternatives: using /usr/bin/python3-unit2 to provide /usr/bin/unit2 (unit2) in auto mode
Setting up netpbm (2:11.03.06-1) ...
Setting up libxt6:armhf (1:1.2.1-1.1) ...
Setting up python3-numpy (1:1.24.2-1) ...
Setting up libcups2:armhf (2.4.7-1) ...
Setting up python3-lxml:armhf (4.9.3-1) ...
Setting up python3-rdflib (6.1.1-2) ...
Setting up python3-contourpy (1.0.7-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up dh-python (6.20231107) ...
Setting up python3-all-dev (3.11.4-5) ...
Setting up libxft2:armhf (2.3.6-1) ...
Setting up libxmu6:armhf (2:1.1.3-3) ...
Setting up python3-scipy (1.10.1-2+rpi1) ...
Setting up python3-cairo:armhf (1.24.0-3) ...
Setting up libxi6:armhf (2:1.8-1) ...
Setting up preview-latex-style (12.2-1) ...
Setting up libtk8.6:armhf (8.6.13-2) ...
Setting up debhelper (13.11.7) ...
Setting up libxaw7:armhf (2:1.0.14-1) ...
Setting up python3-mmtf (1.1.3-1) ...
Setting up fonts-urw-base35 (20200910-7) ...
Setting up python3-pil:armhf (10.0.0-1) ...
Setting up python3-rlpycairo (0.3.0-3) ...
Setting up python3-reportlab (4.0.4-11) ...
Setting up texlive-binaries (2023.20230311.66589-6) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Setting up texlive-base (2023.20231007-1) ...
tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
Setting up libgs10-common (10.02.0~dfsg-2) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Setting up blt (2.5.3+dfsg-4.1) ...
Setting up python3-tk:armhf (3.11.5-1) ...
Setting up texlive-latex-base (2023.20231007-1) ...
Setting up python3-pil.imagetk:armhf (10.0.0-1) ...
Setting up texlive-latex-recommended (2023.20231007-1) ...
Setting up texlive-pictures (2023.20231007-1) ...
Setting up texlive-fonts-recommended (2023.20231007-1) ...
Setting up libgs10:armhf (10.02.0~dfsg-2) ...
Setting up texlive-latex-extra (2023.20231007-2) ...
Setting up ghostscript (10.02.0~dfsg-2) ...
Setting up python3-fonttools (4.38.0-1) ...
Setting up python3-ufolib2 (0.16.0+dfsg1-1) ...
Setting up libheif-plugin-dav1d:armhf (1.17.1-1) ...
Setting up libheif-plugin-libde265:armhf (1.17.1-1) ...
Setting up python3-matplotlib (3.6.3-1) ...
Setting up libheif1:armhf (1.17.1-1) ...
Setting up libmagickcore-6.q16-7:armhf (8:6.9.12.98+dfsg1-3) ...
Setting up libgd3:armhf (2.3.3-9+b1) ...
Setting up emboss-lib (6.6.0+dfsg-12) ...
Setting up libmagickwand-6.q16-7:armhf (8:6.9.12.98+dfsg1-3) ...
Setting up emboss (6.6.0+dfsg-12) ...
Setting up imagemagick-6.q16 (8:6.9.12.98+dfsg1-3) ...
update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode
update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode
update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode
update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode
update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode
update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode
update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode
update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode
update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode
update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode
update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode
update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode
update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode
update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode
update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode
update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode
update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode
update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode
update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode
update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode
update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode
update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode
Setting up hevea (2.36-2) ...
Setting up imagemagick (8:6.9.12.98+dfsg1-3) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
Processing triggers for tex-common (6.18) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep  1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 blt_2.5.3+dfsg-4.1 bsdextrautils_2.39.2-5 bsdutils_1:2.39.2-5 build-essential_12.9 bwa_0.7.17-7 bzip2_1.0.8-5+b2 clustalo_1.2.4-7 clustalw_2.1+lgpl-7 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.7 debianutils_5.14 dh-autoreconf_20 dh-python_6.20231107 dh-strip-nondeterminism_1.13.1-1 dialign_2.2.1-11 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dssp_4.2.2-2 dwz_0.15-1 e2fsprogs_1.47.0-2 emboss_6.6.0+dfsg-12 emboss-data_6.6.0+dfsg-12 emboss-lib_6.6.0+dfsg-12 fakeroot_1.32.1-1 fasttree_2.1.11-2 file_1:5.45-2 findutils_4.9.0-5 flex_2.6.4-8.2 fontconfig-config_2.14.2-6 fonts-dejavu-core_2.37-8 fonts-dejavu-extra_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 fonts-lyx_2.3.7-1 fonts-urw-base35_20200910-7 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-13 gettext-base_0.21-13 ghostscript_10.02.0~dfsg-2 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hevea_2.36-2 hicolor-icon-theme_0.17-2 hostname_3.23+nmu1 imagemagick_8:6.9.12.98+dfsg1-3 imagemagick-6-common_8:6.9.12.98+dfsg1-3 imagemagick-6.q16_8:6.9.12.98+dfsg1-3 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libabsl20220623_20220623.1-3 libacl1_2.3.1-3 libaom3_3.7.0-1 libapache-pom-java_29-2 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libargtable2-0_13-1.1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libavahi-client3_0.8-13 libavahi-common-data_0.8-13 libavahi-common3_0.8-13 libavif16_1.0.1-2 libbinutils_2.41-6+rpi1 libblas3_3.11.0-2 libblkid1_2.39.2-5 libboost-regex1.74.0_1.74.0+ds1-23 libbrotli1_1.0.9-2+b3 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcairo2_1.18.0-1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libcifpp-data_5.0.7.1-3 libcifpp5_5.0.7.1-3 libcom-err2_1.47.0-2 libcommons-logging-java_1.2-4 libcommons-parent-java_56-1 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcups2_2.4.7-1 libcurl3-gnutls_8.4.0-2+rpi1 libdav1d6_1.2.1-2+rpi1 libdb5.3_5.3.28+dfsg2-2 libdbus-1-3_1.14.10-3 libde265-0_1.0.11-1+rpi1+b1 libdebconfclient0_0.271 libdebhelper-perl_13.11.7 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libexpat1-dev_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfftw3-double3_3.3.10-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontbox-java_1:1.8.16-4 libfontconfig1_2.14.2-6 libfontenc1_1:1.1.4-1 libfreetype6_2.13.2+dfsg-1 libfribidi0_1.0.13-3 libgav1-1_0.18.0-1+rpi1+b1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+rpi1 libgcrypt20_1.10.2-3 libgd3_2.3.3-9+b1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.2.0-5+rpi1 libglib2.0-0_2.78.1-2 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgraphite2-3_1.3.14-1 libgs-common_10.02.0~dfsg-2 libgs10_10.02.0~dfsg-2 libgs10-common_10.02.0~dfsg-2 libgssapi-krb5-2_1.20.1-4 libharfbuzz0b_8.0.1-1 libheif-plugin-dav1d_1.17.1-1 libheif-plugin-libde265_1.17.1-1 libheif1_1.17.1-1 libhogweed6_3.9.1-2 libhpdf-2.3.0_2.3.0+dfsg-1 libhts3_1.18+ds-1 libhtscodecs2_1.5.2-1 libice6_2:1.0.10-1 libicu72_72.1-4 libidn12_1.41-1+b1 libidn2-0_2.3.4-1 libijs-0.35_0.35-15.1 libimagequant0_2.17.0-1 libisl23_0.26-3 libjansson4_2.14-2 libjbig0_2.1-6.1 libjbig2dec0_0.19-3+b2 libjpeg62-turbo_1:2.1.5-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_7.2.6-2 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libk5crypto3_1.20.1-4 libkeyutils1_1.6.3-2 libkpathsea6_2023.20230311.66589-6 libkrb5-3_1.20.1-4 libkrb5support0_1.20.1-4 libksba8_1.6.4-2 liblapack3_3.11.0-2 liblbfgsb0_3.0+dfsg.4-1 liblcms2-2_2.14-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblerc4_4.0.0+ds-3 liblmdb0_0.9.31-1 liblocale-gettext-perl_1.07-6 liblqr-1-0_0.4.2-2.1 libltdl7_2.4.7-7 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmagickcore-6.q16-7_8:6.9.12.98+dfsg1-3 libmagickwand-6.q16-7_8:6.9.12.98+dfsg1-3 libmariadb3_1:10.11.3-1+rpi1 libmbedcrypto7_2.28.5-1 libmbedtls14_2.28.5-1 libmbedx509-1_2.28.5-1 libmd0_1.1.0-1 libmount1_2.39.2-5 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses6_6.4+20231016-1 libncursesw6_6.4+20231016-1 libnetpbm11_2:11.03.06-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenjp2-7_2.5.0-2 libp11-kit0_0.25.0-5 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpaper-utils_1.1.29 libpaper1_1.1.29 libpcre2-8-0_10.42-4 libpdfbox-java_1:1.8.16-4 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpng16-16_1.6.40-2 libpotrace0_1.16-2 libpq5_16.0-2 libpsl5_0.21.2-1+b1 libptexenc1_2023.20230311.66589-6 libpython3-all-dev_3.11.4-5 libpython3-dev_3.11.4-5 libpython3-stdlib_3.11.4-5 libpython3.11_3.11.6-3 libpython3.11-dev_3.11.6-3 libpython3.11-minimal_3.11.6-3 libpython3.11-stdlib_3.11.6-3 libqhull-r8.0_2020.2-6 libraqm0_0.10.1-1 librav1e0_0.6.6-3+rpi1 libraw23_0.21.1-7+rpi1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-6+rpi1 libsharpyuv0_1.3.2-0.3 libsm6_2:1.2.3-1 libsmartcols1_2.39.2-5 libsqlite3-0_3.43.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-2 libssl3_3.0.11-1 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 libsub-override-perl_0.09-4 libsvtav1enc1d1_1.7.0+dfsg-2 libsynctex2_2023.20230311.66589-6 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtcl8.6_8.6.13+dfsg-2 libteckit0_2.5.11+ds1-1 libtexlua53-5_2023.20230311.66589-6 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtiff6_4.5.1+git230720-1 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtk8.6_8.6.13-2 libtool_2.4.7-7 libubsan1_13.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.2-5 libwebp7_1.3.2-0.3 libwebpdemux2_1.3.2-0.3 libwebpmux3_1.3.2-0.3 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1 libxaw7_2:1.0.14-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxft2_2.3.6-1 libxi6_2:1.8-1 libxml2_2.9.14+dfsg-1.3 libxmu6_2:1.1.3-3 libxpm4_1:3.5.17-1 libxrender1_1:0.9.10-1.1 libxslt1.1_1.1.35-1 libxss1_1:1.2.3-1 libxt6_1:1.2.1-1.1 libxxhash0_0.8.2-2 libyuv0_0.0~git20230907.cbfb661-1 libzstd1_1.5.5+dfsg2-2 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 mafft_7.505-1 mailcap_3.70+nmu1 make_4.3-4.1 man-db_2.12.0-1 mariadb-common_1:10.11.3-1+rpi1 mawk_1.3.4.20230808-1 media-types_10.1.0 mime-support_3.66 mount_2.39.2-5 mysql-common_5.8+1.1.0 ncbi-blast+_2.12.0+ds-4 ncbi-data_6.1.20170106+dfsg1-10 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 netpbm_2:11.03.06-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 phylip_1:3.697+dfsg-2 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 poppler-data_0.4.12-1 prank_0.0.170427+dfsg-3 preview-latex-style_12.2-1 probcons_1.12-14 python-matplotlib-data_3.6.3-1 python3_3.11.4-5 python3-all_3.11.4-5 python3-all-dev_3.11.4-5 python3-appdirs_1.4.4-4 python3-attr_23.1.0-2 python3-brotli_1.0.9-2+b3 python3-cairo_1.24.0-3 python3-contourpy_1.0.7-1 python3-cycler_0.11.0-1 python3-dateutil_2.8.2-3 python3-decorator_5.1.1-5 python3-dev_3.11.4-5 python3-distutils_3.11.5-1 python3-fonttools_4.38.0-1 python3-freetype_2.4.0-1 python3-fs_2.4.16-2 python3-isodate_0.6.1-1 python3-kiwisolver_1.4.4-1 python3-lib2to3_3.11.5-1 python3-lxml_4.9.3-1 python3-lz4_4.0.2+dfsg-1+b1 python3-matplotlib_3.6.3-1 python3-minimal_3.11.4-5 python3-mmtf_1.1.3-1 python3-mpmath_1.2.1-2 python3-msgpack_1.0.3-3 python3-mysqldb_1.4.6-2+b1 python3-networkx_2.8.8-1 python3-numpy_1:1.24.2-1 python3-packaging_23.1-1 python3-pil_10.0.0-1 python3-pil.imagetk_10.0.0-1 python3-pkg-resources_68.1.2-2 python3-psycopg2_2.9.6-3 python3-pygments_2.15.1+dfsg-1 python3-pyparsing_3.1.1-1 python3-rdflib_6.1.1-2 python3-reportlab_4.0.4-11 python3-rlpycairo_0.3.0-3 python3-scipy_1.10.1-2+rpi1 python3-setuptools_68.1.2-2 python3-six_1.16.0-4 python3-sympy_1.12-6 python3-tk_3.11.5-1 python3-tz_2023.3.post1-1 python3-ufolib2_0.16.0+dfsg1-1 python3-unittest2_1.1.0-9 python3.11_3.11.6-3 python3.11-dev_3.11.6-3 python3.11-minimal_3.11.6-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 samtools_1.18-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-3 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 t1utils_1.41-4 tar_1.34+dfsg-1.2 tex-common_6.18 texlive-base_2023.20231007-1 texlive-binaries_2023.20230311.66589-6 texlive-fonts-recommended_2023.20231007-1 texlive-latex-base_2023.20231007-1 texlive-latex-extra_2023.20231007-2 texlive-latex-recommended_2023.20231007-1 texlive-pictures_2023.20231007-1 tk8.6-blt2.5_2.5.3+dfsg-4.1 tzdata_2023c-10 ucf_3.0043+nmu1 unicode-data_15.1.0-1 usr-is-merged_37 util-linux_2.39.2-5 wise_2.4.1-23 wise-data_2.4.1-23 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+6 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: python-biopython
Binary: python3-biopython, python-biopython-doc, python3-biopython-sql
Architecture: any all
Version: 1.81+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://biopython.org
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-biopython
Vcs-Git: https://salsa.debian.org/med-team/python-biopython.git
Testsuite: autopkgtest
Testsuite-Triggers: @builddeps@, python3-all, python3-setuptools
Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-numpy, flex, python3-reportlab (>= 4.0.4-1~) <!nocheck>, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa <!nocheck>, clustalo <!nocheck>, clustalw <!nocheck>, dialign <!nocheck>, dssp <!nocheck>, emboss <!nocheck>, fasttree <!nocheck>, mafft <!nocheck>, muscle3 [i386 amd64 x32] <!nocheck>, ncbi-blast+ <!nocheck>, phylip <!nocheck>, phyml [any-amd64 any-i386] <!nocheck>, prank <!nocheck>, probcons <!nocheck>, python3-networkx <!nocheck>, python3-mysqldb <!nocheck>, python3-matplotlib <!nocheck>, python3-mmtf <!nocheck>, python3-pil <!nocheck>, python3-rdflib <!nocheck>, python3-psycopg2 <!nocheck>, python3-pygments <!nocheck>, python3-scipy <!nocheck>, python3-setuptools, python3-unittest2 <!nocheck>, raxml [any-amd64 any-i386] <!nocheck>, samtools <!nocheck>, t-coffee <!nocheck>, wise <!nocheck>
Package-List:
 python-biopython-doc deb doc optional arch=all
 python3-biopython deb python optional arch=any
 python3-biopython-sql deb python optional arch=all
Checksums-Sha1:
 d8b39f189078bd119960a3e5c3136e1cc53e4d64 11483844 python-biopython_1.81+dfsg.orig.tar.xz
 0ecf042dbea96f762fb2bad3d6fb15bc0361ff78 20620 python-biopython_1.81+dfsg-2.debian.tar.xz
Checksums-Sha256:
 459868a86c2e47a0cc2f19be1371dd5309474b3106d17093cadebf7abdd03413 11483844 python-biopython_1.81+dfsg.orig.tar.xz
 71bdd29d0cd4a38c9013d227ace769d32a2b1d519bc038eebdbca53a4b53e98b 20620 python-biopython_1.81+dfsg-2.debian.tar.xz
Files:
 67dfa4cf427956d8dbb5be53c2b62d49 11483844 python-biopython_1.81+dfsg.orig.tar.xz
 d40b679986c4d775579138690aae1c06 20620 python-biopython_1.81+dfsg-2.debian.tar.xz
Dgit: 4e33ddc448a7b722c099ee4724bfc231ce864f82 debian archive/debian/1.81+dfsg-2 https://git.dgit.debian.org/python-biopython

-----BEGIN PGP SIGNATURE-----
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=84T4
-----END PGP SIGNATURE-----

gpgv: Signature made Sat Nov 11 15:39:36 2023 UTC
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.81+dfsg-2.dsc: no acceptable signature found
dpkg-source: info: extracting python-biopython in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking python-biopython_1.81+dfsg.orig.tar.xz
dpkg-source: info: unpacking python-biopython_1.81+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying remove_mathml-qname.patch
dpkg-source: info: applying privacy_breach.patch
dpkg-source: info: applying privacy_breach_ie9.patch
dpkg-source: info: applying fix-use-of-unversioned-python.patch
dpkg-source: info: applying reproduciblebuild.patch
dpkg-source: info: applying croak-on-muscle5.patch
dpkg-source: info: applying muscle3.patch
dpkg-source: info: applying port_tutorial_to_muscle3.patch
dpkg-source: info: applying remove-distutils-import.patch
dpkg-source: info: applying python3.12.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-24294010-01d2-45ae-b08a-751d102d18f2
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package python-biopython
dpkg-buildpackage: info: source version 1.81+dfsg-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
	pybuild --clean -i python{version} -p 3.11
I: pybuild base:310: python3.11 setup.py clean 
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
	rm -rf .pybuild/
	find . -name \*.pyc -exec rm {} \;
cd Doc && make distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>/Doc'
( for f in  ; do make clean -C $f ; done )
rm -f Tutorial.aux
rm -f Tutorial.toc
rm -f Tutorial.log
rm -f Tutorial.out
rm -f Tutorial.haux
rm -f Tutorial.htoc
rm -f biopdb_faq.aux
rm -f biopdb_faq.log
rm -f biopdb_faq.out
rm -f Tutorial/*.aux
rm -rf _minted-Tutorial
( for f in  ; do make distclean -C $f ; done )
rm -f version.sh
rm -f biopdb_faq.pdf
rm -f Tutorial.pdf
rm -f Tutorial.html
rm -f Tutorial.txt
rm -f *_motif.gif #output from hacha
make[2]: Leaving directory '/<<PKGBUILDDIR>>/Doc'
rm -f Doc/install/Installation.pdf
rm -f Doc/install/Installation.txt
rm -f Doc/install/Installation.html
rm -f Doc/Tutorial.pdf Doc/biopdb_faq.pdf
rm -f Doc/Tutorial/*.aux
find Doc -name "*.pygtex" -o -name "*.pygstyle" -delete
rm -rf biopython.egg-info
rm -rf .pybuild
if [ -d Tests_avoid ] ; then \
    mv Tests_avoid/* Tests ; \
    rmdir Tests_avoid ; \
fi
rm -rf debian/tmp_tests
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/python3-biopython.substvars debian/python-biopython-doc.substvars debian/python3-biopython-sql.substvars debian/files
	rm -fr -- debian/python3-biopython/ debian/tmp/ debian/python-biopython-doc/ debian/python3-biopython-sql/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
 debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
	pybuild --configure -i python{version} -p 3.11
I: pybuild base:310: python3.11 setup.py config 
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
	pybuild --build -i python{version} -p 3.11
I: pybuild base:310: /usr/bin/python3 setup.py build 
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/File.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/LogisticRegression.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/MarkovModel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/MaxEntropy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/NaiveBayes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/Seq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/SeqFeature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/SeqRecord.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/bgzf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/kNN.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/pairwise2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Affy
copying Bio/Affy/CelFile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Affy
copying Bio/Affy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Affy
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/AlignInfo.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/a2m.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/bed.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/bigbed.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/bigmaf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/bigpsl.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/clustal.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/emboss.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/exonerate.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/fasta.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/hhr.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/interfaces.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/maf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/mauve.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/msf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/nexus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/phylip.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/psl.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/sam.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/stockholm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/tabular.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices
copying Bio/Align/substitution_matrices/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/MsfIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Alphabet
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Application
copying Bio/Application/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Application
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/Applications.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/NCBIXML.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/Record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/CAPS
copying Bio/CAPS/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/CAPS
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster
copying Bio/Cluster/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign
copying Bio/codonalign/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign
copying Bio/codonalign/codonseq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Compass
copying Bio/Compass/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Compass
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/CodonTable.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/IUPACData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/PDBData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/SCOPData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss
copying Bio/Emboss/Applications.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss
copying Bio/Emboss/Primer3.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss
copying Bio/Emboss/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez
copying Bio/Entrez/Parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez
copying Bio/Entrez/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank
copying Bio/GenBank/Record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank
copying Bio/GenBank/Scanner.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank
copying Bio/GenBank/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank
copying Bio/GenBank/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Geo
copying Bio/Geo/Record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Geo
copying Bio/Geo/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Geo
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/Comparative.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/Distribution.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/MarkovModel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/Trainer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/Utilities.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG
copying Bio/KEGG/REST.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG
copying Bio/KEGG/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/mmtfio.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Medline
copying Bio/Medline/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Medline
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/alignace.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/clusterbuster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/mast.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/matrix.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/meme.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/minimal.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/pfm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/thresholds.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/transfac.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/xms.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/applications
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/Nexus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/Nodes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/StandardData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/Trees.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR
copying Bio/NMR/NOEtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR
copying Bio/NMR/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR
copying Bio/NMR/xpktools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway
copying Bio/Pathway/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep
copying Bio/PDB/AbstractPropertyMap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Atom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Chain.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/DSSP.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Dice.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Entity.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/HSExposure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Model.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/NACCESS.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PDBIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PDBList.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PDBParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PICIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PSEA.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Polypeptide.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Residue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/SASA.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/SCADIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Selection.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Structure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Superimposer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/cealign.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/ic_data.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/ic_rebuild.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/internal_coords.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/mmcifio.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/qcprot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/vectors.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype
copying Bio/phenotype/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen
copying Bio/PopGen/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction
copying Bio/Restriction/Restriction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction
copying Bio/Restriction/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Cla.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Des.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Dom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Hie.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Raf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Residues.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/_index.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/GckIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/SnapGeneIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/TwoBitIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/XdnaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/_index.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SwissProt
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/TogoWS
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/CDAO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/Consensus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/NeXML.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/Newick.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/_io.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniGene
copying Bio/UniGene/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniGene
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniProt
copying Bio/UniProt/GOA.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniProt
copying Bio/UniProt/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniProt
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise
copying Bio/Wise/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise
copying Bio/Wise/dnal.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise
copying Bio/Wise/psw.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/BioSeq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/BioSeqDatabase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/DBUtils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/Loader.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL
running egg_info
creating biopython.egg-info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
writing manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are
        already explicitly excluding 'Bio.Align.substitution_matrices.data' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'Bio.Entrez.DTDs' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'Bio.Entrez.DTDs' to be distributed and are
        already explicitly excluding 'Bio.Entrez.DTDs' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'Bio.Entrez.XSDs' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'Bio.Entrez.XSDs' to be distributed and are
        already explicitly excluding 'Bio.Entrez.XSDs' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
copying Bio/cpairwise2module.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio
copying Bio/Align/_aligners.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER22 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER6 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER74 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTN -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTP -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/FENG -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GENETIC -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/HOXD70 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JOHNSON -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JONES -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/LEVIN -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MDM78 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MEGABLAST -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM250 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM30 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM70 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RAO -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RISLER -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/STR -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/TRANS -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Cluster/cluster.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster
copying Bio/Cluster/cluster.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-display1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-format1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-link1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-list1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-math1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-para1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-references1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-section1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivearticle.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/articlemeta.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/backmatter.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/chars.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/common.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-classes.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-mixes.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/display.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSearch_020511.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSpell.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSummary_041029.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/egquery.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/einfo.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/elink.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/elink_020122.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/epost.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esearch.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esummary_gene.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/format.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/htmltable.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsa.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsb.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsc.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsn.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamso.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsr.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isobox.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr1.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr2.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isodia.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk1.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk2.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk4.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat1.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat2.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomfrk.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomopf.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomscr.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isonum.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isopub.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isotech.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/journalmeta.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/link.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/list.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/math.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlalias.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlextra.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/modules.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pmc-1.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/taxon.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-table-1.mod -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/Nexus/cnexus.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/PDB/ccealignmodule.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/kdtrees.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/SeqIO/_twoBitIO.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer
running build_ext
building 'Bio.Align._aligners' extension
creating build
creating build/temp.linux-armv7l-cpython-311
creating build/temp.linux-armv7l-cpython-311/Bio
creating build/temp.linux-armv7l-cpython-311/Bio/Align
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligners.c -o build/temp.linux-armv7l-cpython-311/Bio/Align/_aligners.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/Align/_aligners.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so
building 'Bio.cpairwise2' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-armv7l-cpython-311/Bio/cpairwise2module.o
Bio/cpairwise2module.c: In function ‘_get_match_score’:
Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
   60 |     if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
      |     ^~
In file included from /usr/include/python3.11/Python.h:95,
                 from Bio/cpairwise2module.c:16:
/usr/include/python3.11/ceval.h:27:43: note: declared here
   27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/cpairwise2module.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-armv7l-cpython-311/Bio/Nexus
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-armv7l-cpython-311/Bio/Nexus/cnexus.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-armv7l-cpython-311/Bio/PDB
creating build/temp.linux-armv7l-cpython-311/Bio/PDB/QCPSuperimposer
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armv7l-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-armv7l-cpython-311/Bio/motifs
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-armv7l-cpython-311/Bio/motifs/_pwm.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/motifs/_pwm.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-armv7l-cpython-311/Bio/Cluster
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-armv7l-cpython-311/Bio/Cluster/cluster.o
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armv7l-cpython-311/Bio/Cluster/clustermodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/Cluster/cluster.o build/temp.linux-armv7l-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so
building 'Bio.PDB.kdtrees' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-armv7l-cpython-311/Bio/PDB/kdtrees.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so
building 'Bio.PDB.ccealign' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-armv7l-cpython-311/Bio/PDB/ccealignmodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so
building 'Bio.SeqIO._twoBitIO' extension
creating build/temp.linux-armv7l-cpython-311/Bio/SeqIO
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-armv7l-cpython-311/Bio/SeqIO/_twoBitIO.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so
cd Doc && make
make[2]: Entering directory '/<<PKGBUILDDIR>>/Doc'
sed "s/\@VERSION\@/1.81/g" version.in > version.sh
chmod +x version.sh
hevea -exec ./version.sh -exec xxdate.exe -fix Tutorial.tex
Exclude comment 'comment'
./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009'
./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000'
./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_introduction.tex:97: Warning: Undefined citation: 'dehoon2004'
./Tutorial/chapter_introduction.tex:98: Warning: Undefined citation: 'pritchard2006'
./Tutorial/chapter_introduction.tex:99: Warning: Undefined citation: 'talevich2012'
./Tutorial/chapter_introduction.tex:100: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_introduction.tex:185: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_introduction.tex:191: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced'
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined label: 'sec:connecting-with-biological-databases'
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_quick_start.tex:150: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_quick_start.tex:158: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_quick_start.tex:159: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined label: 'sec:mutable-seq'
./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_objects.tex:157: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_seq_objects.tex:353: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seq_objects.tex:475: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:33: Warning: Undefined label: 'sec:FASTQ-filtering-example'
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:600: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_seq_annot.tex:793: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_annot.tex:805: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer'
./Tutorial/chapter_seq_annot.tex:806: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor'
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seqio.tex:14: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:SeqIO_Online'
./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:43: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_seqio.tex:68: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab'
./Tutorial/chapter_seqio.tex:150: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:306: Warning: Undefined label: 'sec:writing-sequence-files'
./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:329: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:398: Warning: Undefined label: 'sec:SeqIO-index-bgzf'
./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:414: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:509: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_seqio.tex:565: Warning: Undefined label: 'sec:seqio_todict'
./Tutorial/chapter_seqio.tex:571: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:575: Warning: Undefined label: 'sec:SeqIO-index-db'
./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-indexing-discussion'
./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:661: Warning: Undefined label: 'sec:fasta-parsing'
./Tutorial/chapter_seqio.tex:783: Warning: Undefined label: 'sec:fastq-indexing'
./Tutorial/chapter_seqio.tex:804: Warning: Undefined label: 'sec:seqio-todict-functionkey'
./Tutorial/chapter_seqio.tex:866: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_seqio.tex:948: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fastq-conversion'
./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion'
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined label: 'sec:seq-reverse-complement'
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_seqio.tex:1311: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seqio.tex:1412: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_align.tex:31: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument'
./Tutorial/chapter_align.tex:113: Warning: Undefined label: 'sec:alignment-format'
./Tutorial/chapter_align.tex:444: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_align.tex:633: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_align.tex:813: Warning: Undefined label: 'sec:SeqRecord-addition'
./Tutorial/chapter_align.tex:892: Warning: Undefined label: 'sec:subs_mat_ex'
./Tutorial/chapter_align.tex:913: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_align.tex:917: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_align.tex:947: Warning: Undefined label: 'sec:emboss-needle-water'
./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:1093: Warning: Undefined label: 'chapter:phylo'
./Tutorial/chapter_align.tex:1317: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:1492: Warning: Undefined citation: 'durbin1998'
./Tutorial/chapter_align.tex:1505: Warning: Undefined label: 'sec:pairwise-aligner'
./Tutorial/chapter_align.tex:1578: Warning: Undefined citation: 'waterman1987'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-substitution-scores'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1609: Warning: Undefined label: 'sec:pairwise-basic'
./Tutorial/chapter_align.tex:1612: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1613: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1639: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1639: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1668: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1772: Warning: Undefined label: 'table:align-meta-attributes'
./Tutorial/chapter_align.tex:1908: Warning: Undefined label: 'sec:pairwise-examples'
./Tutorial/chapter_align.tex:2424: Warning: Undefined citation: 'kent2002'
./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2725: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:2725: Warning: Undefined label: 'sec:substitution_matrices'
./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:3282: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'henikoff1992'
./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'dayhoff1978'
./Tutorial/chapter_align.tex:3379: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:3379: Warning: Suppressing nested a element
./Tutorial/chapter_align.tex:3391: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio'
./Tutorial/chapter_blast.tex:73: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:133: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:138: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:160: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:169: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:178: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:206: Warning: Undefined label: 'sec:alignment-tools'
./Tutorial/chapter_blast.tex:241: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:287: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:289: Warning: Undefined label: 'sec:running-local-blast'
./Tutorial/chapter_blast.tex:304: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_blast.tex:452: Warning: Undefined label: 'fig:blastrecord'
./Tutorial/chapter_blast.tex:468: Warning: Undefined label: 'fig:psiblastrecord'
./Tutorial/chapter_searchio.tex:739: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_searchio.tex:1089: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_entrez.tex:21: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:60: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:63: Warning: Undefined label: 'sec:BioSQL'
./Tutorial/chapter_entrez.tex:216: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:220: Warning: Undefined label: 'sec:entrez-einfo'
./Tutorial/chapter_entrez.tex:236: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:299: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:419: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:481: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:483: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:565: Warning: Undefined label: 'sec:elink-citations'
./Tutorial/chapter_entrez.tex:571: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:818: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:818: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:940: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1103: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1106: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1110: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1153: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1197: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1197: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1199: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1254: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1289: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1296: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:1297: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:1373: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_entrez.tex:1374: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1434: Warning: Undefined label: 'sec:entrez-search-fetch-genbank'
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:1545: Warning: Undefined label: 'sec:entrez-and-medline'
./Tutorial/chapter_entrez.tex:1550: Warning: Undefined label: 'sec:elink'
./Tutorial/chapter_entrez.tex:1575: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt'
./Tutorial/chapter_uniprot.tex:37: Warning: Undefined label: 'sec:expasy_swissprot'
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt'
./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:345: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_pdb.tex:84: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:275: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:284: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:421: Warning: Undefined label: 'sec:hetero_problems'
./Tutorial/chapter_pdb.tex:466: Warning: Undefined label: 'sec:point_mutations'
./Tutorial/chapter_pdb.tex:483: Warning: Undefined label: 'sec:disordered_atoms'
./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:610: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:657: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:924: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1261: Warning: Undefined label: 'fig:distanceplot'
./Tutorial/chapter_pdb.tex:1383: Warning: Undefined label: 'fig:phepairs'
./Tutorial/chapter_pdb.tex:1455: Warning: Undefined label: 'table:ic-attribs'
./Tutorial/chapter_pdb.tex:1496: Warning: Undefined citation: 'golub1989'
./Tutorial/chapter_pdb.tex:1524: Warning: Undefined citation: 'hamelryck2005'
./Tutorial/chapter_pdb.tex:1559: Warning: Undefined label: 'table:DSSP-codes'
./Tutorial/chapter_pdb.tex:1599: Warning: Undefined label: 'sec:residue_depth'
./Tutorial/chapter_pdb.tex:1602: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1650: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_pdb.tex:1664: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1861: Warning: Undefined citation: 'hamelryck2003b'
./Tutorial/chapter_pdb.tex:1862: Warning: Undefined citation: 'majumdar2005'
./Tutorial/chapter_phylo.tex:9: Warning: Undefined citation: 'talevich2012'
./Tutorial/chapter_phylo.tex:96: Warning: Undefined label: 'fig:phylo-simple-draw'
./Tutorial/chapter_phylo.tex:201: Warning: Undefined label: 'fig:phylo-color-draw'
./Tutorial/chapter_phylo.tex:823: Warning: Undefined label: 'sec:PhyloXML'
./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links'
./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cornish1985'
./Tutorial/chapter_motifs.tex:166: Warning: Undefined citation: 'cavener1987'
./Tutorial/chapter_motifs.tex:542: Warning: Undefined citation: 'bailey1994'
./Tutorial/chapter_motifs.tex:688: Warning: Undefined citation: 'matys2003'
./Tutorial/chapter_motifs.tex:772: Warning: Undefined label: 'table:transfaccodes'
./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004'
./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988'
./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988'
./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989'
./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:278: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:346: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:556: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'kohonen1997'
./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'tamayo1999'
./Tutorial/chapter_cluster.tex:647: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:660: Warning: Undefined citation: 'yeung2001'
./Tutorial/chapter_cluster.tex:668: Warning: Undefined citation: 'golub1971'
./Tutorial/chapter_cluster.tex:802: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:805: Warning: Undefined label: 'sec:distancematrix'
./Tutorial/chapter_cluster.tex:823: Warning: Undefined label: 'sec:clustercentroids'
./Tutorial/chapter_cluster.tex:846: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:871: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:900: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:922: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:954: Warning: Undefined citation: 'hihara2001'
./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'sec:LogisticRegression'
./Tutorial/chapter_learning.tex:277: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegressionTraining'
./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006'
./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006'
./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009'
./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:345: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down'
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002'
./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002'
./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012'
./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:206: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_cookbook.tex:338: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_cookbook.tex:443: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:457: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_cookbook.tex:643: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:646: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_cookbook.tex:801: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:823: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:825: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:1024: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:1418: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1436: Warning: Undefined label: 'sec:consensus'
./Tutorial/chapter_cookbook.tex:1437: Warning: Undefined label: 'sec:pssm'
./Tutorial/chapter_cookbook.tex:1438: Warning: Undefined label: 'sec:getting_info_content'
./Tutorial/chapter_cookbook.tex:1439: Warning: Undefined label: 'sec:sub_matrix'
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1640: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_testing.tex:55: Warning: Undefined label: 'sec:doctest'
./Tutorial/chapter_testing.tex:282: Warning: Undefined label: 'sec:doctest'
./Tutorial/chapter_contributing.tex:32: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:75: Warning: Undefined label: 'chapter:testing'
./Tutorial/chapter_contributing.tex:91: Warning: Undefined label: 'chapter:testing'
./Tutorial/chapter_appendix.tex:91: Warning: Undefined label: 'sec:SeqIO_compressed'
HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right.
Run, run, again...
Exclude comment 'comment'
./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced'
./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:3379: Warning: Suppressing nested a element
./Tutorial/chapter_entrez.tex:1103: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1106: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1197: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1197: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:924: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1602: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1664: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode
Fixpoint reached in 2 step(s)
hevea -exec ./version.sh -exec xxdate.exe -fix -text Tutorial.tex
Exclude comment 'comment'
./Tutorial.tex:73: Warning: tt_mode is an empty style
./Tutorial.tex:100: Warning: Application of '\'' on 'n' failed
./Tutorial.htoc:378: Warning: Application of '\"' on 'i' failed
./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced'
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:84: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:118: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:296: Warning: Command not found: \downarrow
./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:120: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:139: Warning: line too long
./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:197: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:218: Warning: line too long
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:508: Warning: line too long
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:668: Warning: line too long
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: line too long
./Tutorial/chapter_seq_annot.tex:704: Warning: line too long
./Tutorial/chapter_seq_annot.tex:704: Warning: line too long
./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:715: Warning: line too long
./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:725: Warning: line too long
./Tutorial/chapter_seq_annot.tex:746: Warning: line too long
./Tutorial/chapter_seq_annot.tex:746: Warning: line too long
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:880: Warning: line too long
./Tutorial/chapter_seq_annot.tex:897: Warning: line too long
./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1: Warning: line too long
./Tutorial/chapter_seqio.tex:1: Warning: line too long
./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:150: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:248: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:550: Warning: line too long
./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:850: Warning: line too long
./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1818: Warning: overfull line in array : array too wide
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2295: Warning: line too long
./Tutorial/chapter_align.tex:2311: Warning: line too long
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2428: Warning: line too long
./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3448: Warning: line too long
./Tutorial/chapter_align.tex:3450: Warning: line too long
./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:1: Warning: line too long
./Tutorial/chapter_blast.tex:1: Warning: line too long
./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:45: Warning: line too long
./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:440: Warning: line too long
./Tutorial/chapter_blast.tex:442: Warning: line too long
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:456: Warning: Image in text
./Tutorial/chapter_blast.tex:472: Warning: Image in text
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1: Warning: line too long
./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:29: Warning: '_' occurring outside math mode
./Tutorial/chapter_searchio.tex:31: Warning: '_' occurring outside math mode
./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:733: Warning: line too long
./Tutorial/chapter_searchio.tex:735: Warning: line too long
./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:966: Warning: line too long
./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:987: Warning: line too long
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1085: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1085: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1089: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1089: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1103: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1106: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1124: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1124: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1197: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1197: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1296: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1296: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:1: Warning: line too long
./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:31: Warning: line too long
./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:497: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:1: Warning: line too long
./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:288: Warning: Image in text
./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:924: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1275: Warning: Image in text
./Tutorial/chapter_pdb.tex:1294: Warning: line too long
./Tutorial/chapter_pdb.tex:1388: Warning: Image in text
./Tutorial/chapter_pdb.tex:1473: Warning: overfull line in array : array too wide
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1602: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1664: Warning: '_' occurring outside math mode
./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:107: Warning: Image in text
./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:208: Warning: Image in text
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:388: Warning: line too long
./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:401: Warning: Image in text
./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1: Warning: line too long
./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:550: Warning: line too long
./Tutorial/chapter_motifs.tex:552: Warning: line too long
./Tutorial/chapter_motifs.tex:558: Warning: line too long
./Tutorial/chapter_motifs.tex:560: Warning: line too long
./Tutorial/chapter_motifs.tex:569: Warning: line too long
./Tutorial/chapter_motifs.tex:573: Warning: line too long
./Tutorial/chapter_motifs.tex:575: Warning: line too long
./Tutorial/chapter_motifs.tex:584: Warning: line too long
./Tutorial/chapter_motifs.tex:586: Warning: line too long
./Tutorial/chapter_motifs.tex:587: Warning: line too long
./Tutorial/chapter_motifs.tex:589: Warning: line too long
./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1567: Warning: '_' occurring outside math mode
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:112: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cluster.tex:115: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:607: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:611: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:616: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:711: Warning: line too long
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:749: Warning: overfull line in array : array too wide
./Tutorial/chapter_cluster.tex:749: Warning: line too long
./Tutorial/chapter_cluster.tex:749: Warning: line too long
./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:26: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_learning.tex:36: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"]
./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"]
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_learning.tex:70: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:397: Warning: Application of '\"' on 'i' failed
./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:68: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:132: Warning: Image in text
./Tutorial/chapter_graphics.tex:132: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:163: Warning: Image in text
./Tutorial/chapter_graphics.tex:163: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:325: Warning: Image in text
./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:396: Warning: Image in text
./Tutorial/chapter_graphics.tex:396: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: Image in text
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: Image in text
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:564: Warning: Image in text
./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:566: Warning: Image in text
./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:728: Warning: Image in text
./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:890: Warning: Image in text
./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:923: Warning: Image in text
./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1035: Warning: line too long
./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1110: Warning: Image in text
./Tutorial/chapter_graphics.tex:1110: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:1125: Warning: line too long
./Tutorial/chapter_graphics.tex:1190: Warning: Image in text
./Tutorial/chapter_graphics.tex:1190: Warning: '_' occurring outside math mode
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:10: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:452: Warning: line too long
./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:561: Warning: line too long
./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:804: Warning: line too long
./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:904: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1053: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1094: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1094: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1127: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1163: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1163: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1211: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1265: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1265: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1341: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1363: Warning: line too long
./Tutorial/chapter_cookbook.tex:1364: Warning: line too long
./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1412: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1743: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:222: Warning: line too long
./Tutorial/chapter_testing.tex:275: Warning: line too long
./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:11: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:58: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:58: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:70: Warning: '_' occurring outside math mode
./Tutorial/chapter_appendix.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial.tex:126: Warning: line too long
./Tutorial.tex:137: Warning: Application of '\'' on 'e' failed
./Tutorial.tex:137: Warning: Application of '\'' on 'o' failed
./Tutorial.tex:141: Warning: Application of '\"' on 'u' failed
./Tutorial.tex:215: Warning: Application of '\"' on 'o' failed
./Tutorial.tex:215: Warning: Application of '\"' on 'u' failed
HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right.
Run, run, again...
Exclude comment 'comment'
./Tutorial.tex:73: Warning: tt_mode is an empty style
./Tutorial.haux:567: Giving up command: \@hevea@cbrace
./Tutorial.tex:73: Giving up command: \input
./Tutorial.tex:73: Warning: Failure while reading .haux
./Tutorial.tex:100: Warning: Application of '\'' on 'n' failed
./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009'
./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000'
./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:97: Warning: Undefined citation: 'dehoon2004'
./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:98: Warning: Undefined citation: 'pritchard2006'
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined citation: 'talevich2012'
./Tutorial/chapter_introduction.tex:100: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:185: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced'
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined label: 'sec:connecting-with-biological-databases'
./Tutorial/chapter_quick_start.tex:84: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:118: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:150: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_quick_start.tex:158: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_quick_start.tex:159: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined label: 'sec:mutable-seq'
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:157: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:296: Warning: Command not found: \downarrow
./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:353: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:475: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:33: Warning: Undefined label: 'sec:FASTQ-filtering-example'
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:120: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:139: Warning: line too long
./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:197: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:218: Warning: line too long
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:508: Warning: line too long
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:600: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:668: Warning: line too long
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: line too long
./Tutorial/chapter_seq_annot.tex:704: Warning: line too long
./Tutorial/chapter_seq_annot.tex:704: Warning: line too long
./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:715: Warning: line too long
./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:725: Warning: line too long
./Tutorial/chapter_seq_annot.tex:746: Warning: line too long
./Tutorial/chapter_seq_annot.tex:746: Warning: line too long
./Tutorial/chapter_seq_annot.tex:793: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_annot.tex:805: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer'
./Tutorial/chapter_seq_annot.tex:806: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor'
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:880: Warning: line too long
./Tutorial/chapter_seq_annot.tex:897: Warning: line too long
./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1: Warning: line too long
./Tutorial/chapter_seqio.tex:1: Warning: line too long
./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:SeqIO_Online'
./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:43: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:68: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab'
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:150: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:150: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:248: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:306: Warning: Undefined label: 'sec:writing-sequence-files'
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:329: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:398: Warning: Undefined label: 'sec:SeqIO-index-bgzf'
./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:414: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:509: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:550: Warning: line too long
./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:565: Warning: Undefined label: 'sec:seqio_todict'
./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:571: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:575: Warning: Undefined label: 'sec:SeqIO-index-db'
./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-indexing-discussion'
./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined label: 'sec:fasta-parsing'
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:783: Warning: Undefined label: 'sec:fastq-indexing'
./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:804: Warning: Undefined label: 'sec:seqio-todict-functionkey'
./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:850: Warning: line too long
./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:866: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:948: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fastq-conversion'
./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion'
./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined label: 'sec:seq-reverse-complement'
./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_seqio.tex:1311: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1412: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:31: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument'
./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined label: 'sec:alignment-format'
./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:444: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:813: Warning: Undefined label: 'sec:SeqRecord-addition'
./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined label: 'sec:subs_mat_ex'
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:917: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:947: Warning: Undefined label: 'sec:emboss-needle-water'
./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1093: Warning: Undefined label: 'chapter:phylo'
./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1317: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1492: Warning: Undefined citation: 'durbin1998'
./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1505: Warning: Undefined label: 'sec:pairwise-aligner'
./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1578: Warning: Undefined citation: 'waterman1987'
./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-substitution-scores'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined label: 'sec:pairwise-basic'
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1612: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1613: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined label: 'table:align-meta-attributes'
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1818: Warning: overfull line in array : array too wide
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined label: 'sec:pairwise-examples'
./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2295: Warning: line too long
./Tutorial/chapter_align.tex:2311: Warning: line too long
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined citation: 'kent2002'
./Tutorial/chapter_align.tex:2428: Warning: line too long
./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2725: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:2725: Warning: Undefined label: 'sec:substitution_matrices'
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3282: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'henikoff1992'
./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'dayhoff1978'
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3379: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3448: Warning: line too long
./Tutorial/chapter_align.tex:3450: Warning: line too long
./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:1: Warning: line too long
./Tutorial/chapter_blast.tex:1: Warning: line too long
./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio'
./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:45: Warning: line too long
./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:73: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:133: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:138: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:160: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:169: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:178: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:206: Warning: Undefined label: 'sec:alignment-tools'
./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:241: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:287: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:289: Warning: Undefined label: 'sec:running-local-blast'
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:304: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:440: Warning: line too long
./Tutorial/chapter_blast.tex:442: Warning: line too long
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined label: 'fig:blastrecord'
./Tutorial/chapter_blast.tex:456: Warning: Image in text
./Tutorial/chapter_blast.tex:468: Warning: Undefined label: 'fig:psiblastrecord'
./Tutorial/chapter_blast.tex:472: Warning: Image in text
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1: Warning: line too long
./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:29: Warning: '_' occurring outside math mode
./Tutorial/chapter_searchio.tex:31: Warning: '_' occurring outside math mode
./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:733: Warning: line too long
./Tutorial/chapter_searchio.tex:735: Warning: line too long
./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:739: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:966: Warning: line too long
./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1089: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:21: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:60: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:63: Warning: Undefined label: 'sec:BioSQL'
./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:216: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:220: Warning: Undefined label: 'sec:entrez-einfo'
./Tutorial/chapter_entrez.tex:236: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:299: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:565: Warning: Undefined label: 'sec:elink-citations'
./Tutorial/chapter_entrez.tex:571: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:818: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:818: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:940: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:987: Warning: line too long
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1085: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1085: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1089: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1089: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1103: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1106: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1110: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1124: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1124: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1153: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1197: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1197: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1199: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1254: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1289: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1296: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1296: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1296: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:1297: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1349: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:1373: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_entrez.tex:1374: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1434: Warning: Undefined label: 'sec:entrez-search-fetch-genbank'
./Tutorial/chapter_entrez.tex:1435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1545: Warning: Undefined label: 'sec:entrez-and-medline'
./Tutorial/chapter_entrez.tex:1545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1550: Warning: Undefined label: 'sec:elink'
./Tutorial/chapter_entrez.tex:1575: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_uniprot.tex:1: Warning: line too long
./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt'
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:31: Warning: line too long
./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:37: Warning: Undefined label: 'sec:expasy_swissprot'
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt'
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:345: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:497: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:1: Warning: line too long
./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:84: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:275: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:284: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:288: Warning: Image in text
./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:421: Warning: Undefined label: 'sec:hetero_problems'
./Tutorial/chapter_pdb.tex:466: Warning: Undefined label: 'sec:point_mutations'
./Tutorial/chapter_pdb.tex:483: Warning: Undefined label: 'sec:disordered_atoms'
./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:610: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:657: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:924: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1261: Warning: Undefined label: 'fig:distanceplot'
./Tutorial/chapter_pdb.tex:1275: Warning: Image in text
./Tutorial/chapter_pdb.tex:1294: Warning: line too long
./Tutorial/chapter_pdb.tex:1383: Warning: Undefined label: 'fig:phepairs'
./Tutorial/chapter_pdb.tex:1388: Warning: Image in text
./Tutorial/chapter_pdb.tex:1455: Warning: Undefined label: 'table:ic-attribs'
./Tutorial/chapter_pdb.tex:1473: Warning: overfull line in array : array too wide
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1473: Warning: line too long
./Tutorial/chapter_pdb.tex:1496: Warning: Undefined citation: 'golub1989'
./Tutorial/chapter_pdb.tex:1524: Warning: Undefined citation: 'hamelryck2005'
./Tutorial/chapter_pdb.tex:1559: Warning: Undefined label: 'table:DSSP-codes'
./Tutorial/chapter_pdb.tex:1599: Warning: Undefined label: 'sec:residue_depth'
./Tutorial/chapter_pdb.tex:1602: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1650: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_pdb.tex:1664: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1861: Warning: Undefined citation: 'hamelryck2003b'
./Tutorial/chapter_pdb.tex:1862: Warning: Undefined citation: 'majumdar2005'
./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:9: Warning: Undefined citation: 'talevich2012'
./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined label: 'fig:phylo-simple-draw'
./Tutorial/chapter_phylo.tex:107: Warning: Image in text
./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:201: Warning: Undefined label: 'fig:phylo-color-draw'
./Tutorial/chapter_phylo.tex:208: Warning: Image in text
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:388: Warning: line too long
./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:401: Warning: Image in text
./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:823: Warning: Undefined label: 'sec:PhyloXML'
./Tutorial/chapter_motifs.tex:1: Warning: line too long
./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links'
./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cornish1985'
./Tutorial/chapter_motifs.tex:166: Warning: Undefined citation: 'cavener1987'
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:542: Warning: Undefined citation: 'bailey1994'
./Tutorial/chapter_motifs.tex:550: Warning: line too long
./Tutorial/chapter_motifs.tex:552: Warning: line too long
./Tutorial/chapter_motifs.tex:558: Warning: line too long
./Tutorial/chapter_motifs.tex:560: Warning: line too long
./Tutorial/chapter_motifs.tex:569: Warning: line too long
./Tutorial/chapter_motifs.tex:573: Warning: line too long
./Tutorial/chapter_motifs.tex:575: Warning: line too long
./Tutorial/chapter_motifs.tex:584: Warning: line too long
./Tutorial/chapter_motifs.tex:586: Warning: line too long
./Tutorial/chapter_motifs.tex:587: Warning: line too long
./Tutorial/chapter_motifs.tex:589: Warning: line too long
./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:688: Warning: Undefined citation: 'matys2003'
./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:772: Warning: Undefined label: 'table:transfaccodes'
./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1567: Warning: '_' occurring outside math mode
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004'
./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988'
./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988'
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:112: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cluster.tex:115: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989'
./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:346: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:556: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'kohonen1997'
./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'tamayo1999'
./Tutorial/chapter_cluster.tex:607: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:611: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:616: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:647: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:660: Warning: Undefined citation: 'yeung2001'
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined citation: 'golub1971'
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:711: Warning: line too long
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:749: Warning: overfull line in array : array too wide
./Tutorial/chapter_cluster.tex:749: Warning: line too long
./Tutorial/chapter_cluster.tex:749: Warning: line too long
./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:802: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:805: Warning: Undefined label: 'sec:distancematrix'
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined label: 'sec:clustercentroids'
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:900: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:922: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined citation: 'hihara2001'
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:26: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_learning.tex:36: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"]
./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"]
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:70: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'sec:LogisticRegression'
./Tutorial/chapter_learning.tex:277: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegressionTraining'
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:397: Warning: Application of '\"' on 'i' failed
./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006'
./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006'
./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009'
./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_graphics.tex:68: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:132: Warning: Image in text
./Tutorial/chapter_graphics.tex:132: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:163: Warning: Image in text
./Tutorial/chapter_graphics.tex:163: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:325: Warning: Image in text
./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:345: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:396: Warning: Image in text
./Tutorial/chapter_graphics.tex:396: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: Image in text
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: Image in text
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down'
./Tutorial/chapter_graphics.tex:564: Warning: Image in text
./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:566: Warning: Image in text
./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002'
./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_graphics.tex:728: Warning: Image in text
./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002'
./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:890: Warning: Image in text
./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:923: Warning: Image in text
./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012'
./Tutorial/chapter_graphics.tex:1035: Warning: line too long
./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1110: Warning: Image in text
./Tutorial/chapter_graphics.tex:1110: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:1125: Warning: line too long
./Tutorial/chapter_graphics.tex:1190: Warning: Image in text
./Tutorial/chapter_graphics.tex:1190: Warning: '_' occurring outside math mode
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:10: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:206: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:338: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:443: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:452: Warning: line too long
./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:457: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_cookbook.tex:561: Warning: line too long
./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:643: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:646: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:801: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:804: Warning: line too long
./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:823: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:825: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:904: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1024: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1053: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1094: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1094: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1127: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1163: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1163: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1211: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1265: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1265: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1341: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1363: Warning: line too long
./Tutorial/chapter_cookbook.tex:1364: Warning: line too long
./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1412: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1418: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1436: Warning: Undefined label: 'sec:consensus'
./Tutorial/chapter_cookbook.tex:1437: Warning: Undefined label: 'sec:pssm'
./Tutorial/chapter_cookbook.tex:1438: Warning: Undefined label: 'sec:getting_info_content'
./Tutorial/chapter_cookbook.tex:1439: Warning: Undefined label: 'sec:sub_matrix'
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1640: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1743: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:55: Warning: Undefined label: 'sec:doctest'
./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:222: Warning: line too long
./Tutorial/chapter_testing.tex:275: Warning: line too long
./Tutorial/chapter_testing.tex:282: Warning: Undefined label: 'sec:doctest'
./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:11: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:32: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:58: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:58: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:70: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:75: Warning: Undefined label: 'chapter:testing'
./Tutorial/chapter_contributing.tex:91: Warning: Undefined label: 'chapter:testing'
./Tutorial/chapter_appendix.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:91: Warning: Undefined label: 'sec:SeqIO_compressed'
./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_appendix.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial.tex:126: Warning: line too long
./Tutorial.tex:137: Warning: Application of '\'' on 'e' failed
./Tutorial.tex:137: Warning: Application of '\'' on 'o' failed
./Tutorial.tex:141: Warning: Application of '\"' on 'u' failed
./Tutorial.tex:215: Warning: Application of '\"' on 'o' failed
./Tutorial.tex:215: Warning: Application of '\"' on 'u' failed
Fixpoint reached in 2 step(s)
pdflatex --shell-escape "\def\bpversion{1.81}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2023-06-01> patch level 1
L3 programming layer <2023-08-29>
(./Tutorial.tex (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty)
(/usr/share/texmf/tex/latex/misc/hevea.sty
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') Excluding comment 'rawhtml'
Excluding comment 'htmlonly')
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/lineno/lineno.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/shellesc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/ifplatform/ifplatform.sty
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))
(/usr/share/texlive/texmf-dist/tex/generic/catchfile/catchfile.sty
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty))
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty) (./Tutorial.w18)
) (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.sty
(/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.tex))
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 70.

(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))/usr/bin/pygmentize

(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file Tutorial.aux.
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
Excluding 'htmlonly' comment. Excluding 'rawhtml' comment. [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map} <./images/biopython_logo.pdf>]
No file Tutorial.toc.

pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has 
been already used, duplicate ignored
<to be read again> 
                   \relax 
l.102 \include{Tutorial/chapter_introduction}
                                              [1]
(./Tutorial/chapter_introduction.tex
Chapter 1.
[2]

LaTeX Warning: Citation `cock2009' on page 3 undefined on input line 91.


LaTeX Warning: Citation `chapman2000' on page 3 undefined on input line 95.


LaTeX Warning: Citation `hamelryck2003a' on page 3 undefined on input line 96.


LaTeX Warning: Citation `dehoon2004' on page 3 undefined on input line 97.


LaTeX Warning: Citation `pritchard2006' on page 3 undefined on input line 98.


LaTeX Warning: Citation `talevich2012' on page 3 undefined on input line 99.


LaTeX Warning: Citation `cock2010' on page 3 undefined on input line 100.

[3] Excluding 'rawhtml' comment.
Underfull \hbox (badness 10000) in paragraph at lines 122--128


Underfull \hbox (badness 10000) in paragraph at lines 134--136

(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/C3217FD04973F24516F5530BB525A22CBD02851C2FB632864165FCA4920
46548.pygtex) [4 <./images/biopython_logo_old.jpg>]

LaTeX Warning: Reference `sec:seq-comparison' on page 5 undefined on input line
 185.


Overfull \hbox (2.99303pt too wide) in paragraph at lines 187--189
\OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor
t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or
 see [][]$\OT1/cmtt/m/n/10 http : / / biopython .

LaTeX Warning: Reference `sec:appendix-handles' on page 5 undefined on input li
ne 191.

[5]) [6] (./Tutorial/chapter_quick_start.tex
Chapter 2.

LaTeX Warning: Reference `chapter:cookbook' on page 7 undefined on input line 1
4.


LaTeX Warning: Reference `chapter:advanced' on page 7 undefined on input line 1
4.


LaTeX Warning: Reference `chapter:seq_objects' on page 7 undefined on input lin
e 19.


(./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612CBD02851C2FB632864165FCA4920
46548.pygtex [7])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535ABBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 8 undefined on input line 45.


LaTeX Warning: Reference `sec:sequence-parsing' on page 8 undefined on input li
ne 65.


LaTeX Warning: Reference `chapter:entrez' on page 8 undefined on input line 65.



LaTeX Warning: Reference `chapter:uniprot' on page 8 undefined on input line 65
.


LaTeX Warning: Reference `sec:align_clustal' on page 8 undefined on input line 
65.

[8]

LaTeX Warning: Reference `chapter:seqio' on page 9 undefined on input line 72.


LaTeX Warning: Reference `sec:connecting-with-biological-databases' on page 9 u
ndefined on input line 79.


(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B0213346781855BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26DBD02851C2FB632864165FCA4920
46548.pygtex [9])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F2BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 10 undefined on input line 145
.


LaTeX Warning: Reference `chapter:align' on page 10 undefined on input line 145
.


LaTeX Warning: Reference `chapter:cookbook' on page 10 undefined on input line 
150.


LaTeX Warning: Reference `chapter:entrez' on page 10 undefined on input line 15
8.


LaTeX Warning: Reference `chapter:uniprot' on page 10 undefined on input line 1
59.

[10]

LaTeX Warning: Reference `chapter:cookbook' on page 11 undefined on input line 
169.

) [11] (./Tutorial/chapter_seq_objects.tex
Chapter 3.

LaTeX Warning: Reference `chapter:seq_annot' on page 12 undefined on input line
 5.


LaTeX Warning: Reference `chapter:seqio' on page 12 undefined on input line 5.


(./_minted-Tutorial/048D805D0CE39D0271B0A9A9F6FA0B90BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDCBD02851C2FB632864165FCA4920
46548.pygtex) [12]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0F44B540F3531194878FC29AF017902BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A4BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:mutable-seq' on page 13 undefined on input line 8
6.


(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E97622504BD02851C2FB632864165FCA4920
46548.pygtex [13])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E36BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D9386420BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79ABD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-format' on page 14 undefined on input l
ine 155.


LaTeX Warning: Reference `chapter:seqio' on page 14 undefined on input line 157
.


(./_minted-Tutorial/732D927996C79742AC990312B3D6EEB0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C270BD02851C2FB632864165FCA4920
46548.pygtex [14])
(./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC47BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D394BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8DBD02851C2FB632864165FCA4920
46548.pygtex [15])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF17BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 16 undefined on
 input line 278.


(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC0BD02851C2FB632864165FCA4920
46548.pygtex [16])
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C8753BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B386BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:seq-module-functions' on page 17 undefined on inp
ut line 353.


(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A70BD02851C2FB632864165FCA4920
46548.pygtex [17])
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF82BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD64BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF98BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE79BD02851C2FB632864165FCA4920
46548.pygtex [18])
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B55990BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqIO-translate' on page 19 undefined on input li
ne 469.


LaTeX Warning: Reference `sec:seq-module-functions' on page 19 undefined on inp
ut line 475.


(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874DBD02851C2FB632864165FCA4920
46548.pygtex [19])
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/06DBC59F2EAD33E7A951888537876615BD02851C2FB632864165FCA4920
46548.pygtex) [20]
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE6BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:seq-to-string' on page 21 undefined on input line
 598.


(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C338BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CB669566ECC2CFEDC7429F829576A
D0DC6.pygtex [21])
(./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E84BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DFDB859800920408E228736AD921B5DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B040BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE451BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2EBD02851C2FB632864165FCA4920
46548.pygtex [22])
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CBBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:seq-to-string' on page 23 undefined on input line
 741.


(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C0BD02851C2FB632864165FCA4920
46548.pygtex)) [23] [24] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

LaTeX Warning: Reference `chapter:seq_objects' on page 25 undefined on input li
ne 4.


LaTeX Warning: Reference `chapter:seqio' on page 25 undefined on input line 4.


(./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC809BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:seq_objects' on page 25 undefined on input li
ne 20.


LaTeX Warning: Reference `chapter:seqio' on page 25 undefined on input line 20.



LaTeX Warning: Reference `sec:FASTQ-filtering-example' on page 25 undefined on 
input line 33.

[25]

LaTeX Warning: Reference `sec:seq_features' on page 26 undefined on input line 
37.


LaTeX Warning: Reference `chapter:seqio' on page 26 undefined on input line 47.



(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D407BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC2BD02851C2FB632864165FCA4920
46548.pygtex [26])
(./_minted-Tutorial/510764EE0BB38AD6C688E71989677507669566ECC2CFEDC7429F829576A
D0DC6.pygtex)

LaTeX Warning: Reference `chapter:quick_start' on page 27 undefined on input li
ne 130.


LaTeX Warning: Reference `chapter:seqio' on page 27 undefined on input line 132
.


(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D849822BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD2085BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9669566ECC2CFEDC7429F829576A
D0DC6.pygtex [27])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A669566ECC2CFEDC7429F829576A
D0DC6.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 28 undefined on input line 211
.


(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA601BD02851C2FB632864165FCA4920
46548.pygtex [28])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F926BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0DBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:seq_features' on page 29 undefined on input line 
275.


LaTeX Warning: Reference `sec:locations' on page 29 undefined on input line 284
.


LaTeX Warning: Reference `sec:locations' on page 29 undefined on input line 292
.

[29] [30]
(./_minted-Tutorial/AD47AD29D6F7927F9406BE5609676388BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F3BD02851C2FB632864165FCA4920
46548.pygtex [31])
(./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A1BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:locations' on page 32 undefined on input line 502
.


(./_minted-Tutorial/D86C559003980DC8749AF92530435DFDBD02851C2FB632864165FCA4920
46548.pygtex) [32]
(./_minted-Tutorial/1C0A562378DEEE8E210765437B3E1700BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B49BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C75BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0C3ED75879971F09D72A92585654A32CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E3920BD02851C2FB632864165FCA4920
46548.pygtex [33])
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312DBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:seq-comparison' on page 34 undefined on input lin
e 600.


LaTeX Warning: Reference `sec:locations' on page 34 undefined on input line 608
.


(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F9689BD02851C2FB632864165FCA4920
46548.pygtex [34])

LaTeX Warning: Reference `chapter:seqio' on page 35 undefined on input line 648
.


LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 35 undefined on i
nput line 651.


(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B2340BD02851C2FB632864165FCA4920
46548.pygtex [35])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEBBD02851C2FB632864165FCA4920
46548.pygtex [36])
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A85BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B311BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D2457BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-format' on page 37 undefined on input l
ine 793.


(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF82BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:FASTQ-slicing-off-primer' on page 37 undefined on
 input line 805.


LaTeX Warning: Reference `sec:FASTQ-slicing-off-adaptor' on page 37 undefined o
n input line 806.


LaTeX Warning: Reference `chapter:seqio' on page 37 undefined on input line 819
.


(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDFBD02851C2FB632864165FCA4920
46548.pygtex [37])
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF1718501669BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1BBD02851C2FB632864165FCA4920
46548.pygtex [38])
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED36BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E7BD02851C2FB632864165FCA4920
46548.pygtex) [39]
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B63BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B8793BD02851C2FB632864165FCA4920
46548.pygtex)) [40] (./Tutorial/chapter_seqio.tex
Chapter 5.

LaTeX Warning: Reference `chapter:quick_start' on page 41 undefined on input li
ne 4.


LaTeX Warning: Reference `chapter:seq_annot' on page 41 undefined on input line
 4.


(./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D498BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:seq_annot' on page 41 undefined on input line
 12.


LaTeX Warning: Reference `chapter:seq_objects' on page 41 undefined on input li
ne 12.


LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 41 undefined on in
put line 14.


LaTeX Warning: Reference `sec:SeqIO_Online' on page 41 undefined on input line 
22.


LaTeX Warning: Reference `sec:appendix-handles' on page 41 undefined on input l
ine 22.


(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB6789543DFECA235A69AE23006BA05B
4EB70.pygtex [41])

LaTeX Warning: Reference `sec:sequence-parsing' on page 42 undefined on input l
ine 43.


(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE5009549543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB21BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:sequence-parsing-plus-pylab' on page 42 undefined
 on input line 68.


(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F19543DFECA235A69AE23006BA05B
4EB70.pygtex [42])
(./_minted-Tutorial/C82398A4A04383A063D2E648811230529543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [43]

LaTeX Warning: Reference `chapter:seq_annot' on page 44 undefined on input line
 150.


(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD1622219543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD829543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE6BD02851C2FB632864165FCA4920
46548.pygtex [44])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E734519543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9562C263804C6DD613F075A435553A9FBD02851C2FB632864165FCA4920
46548.pygtex [45])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C91BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:writing-sequence-files' on page 46 undefined on i
nput line 306.


(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579DBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:appendix-handles' on page 46 undefined on input l
ine 329.


(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/23394A4616015FFE4619934E98424178BD02851C2FB632864165FCA4920
46548.pygtex [46])
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C09BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqIO-index-bgzf' on page 47 undefined on input l
ine 398.


LaTeX Warning: Reference `sec:efetch' on page 47 undefined on input line 414.

[47]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD4769543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD89543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D79543DFECA235A69AE23006BA05B
4EB70.pygtex [48])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D669566ECC2CFEDC7429F829576A
D0DC6.pygtex)

LaTeX Warning: Reference `chapter:entrez' on page 49 undefined on input line 50
4.


LaTeX Warning: Reference `sec:entrez-guidelines' on page 49 undefined on input 
line 504.


LaTeX Warning: Reference `chapter:uniprot' on page 49 undefined on input line 5
09.


(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A49543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989FBD02851C2FB632864165FCA4920
46548.pygtex [49])

LaTeX Warning: Reference `sec:seqio_todict' on page 50 undefined on input line 
565.


LaTeX Warning: Reference `sec:SeqIO-index' on page 50 undefined on input line 5
71.


LaTeX Warning: Reference `sec:SeqIO-index-db' on page 50 undefined on input lin
e 575.


LaTeX Warning: Reference `sec:SeqIO-indexing-discussion' on page 50 undefined o
n input line 578.


LaTeX Warning: Reference `sec:SeqIO-index' on page 50 undefined on input line 5
88.


(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB03BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF6BD02851C2FB632864165FCA4920
46548.pygtex [50])
(./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F669566ECC2CFEDC7429F829576A
D0DC6.pygtex)

LaTeX Warning: Reference `sec:fasta-parsing' on page 51 undefined on input line
 661.


(./_minted-Tutorial/55430EAFE498E385842834603E0B8C869543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB89543DFECA235A69AE23006BA05B
4EB70.pygtex [51])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C178893BD02851C2FB632864165FCA4920
46548.pygtex) [52]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C78BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF4065BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A364BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:fastq-indexing' on page 53 undefined on input lin
e 783.


(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:seqio-todict-functionkey' on page 53 undefined on
 input line 804.


(./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920
46548.pygtex [53])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853
\OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org /
 pub / databases / uniprot / current _ release / knowledgebase / complete /

(./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqIO-sort' on page 54 undefined on input line 86
6.


Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894
[]\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u
p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1
/cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76
9EADB.pygtex [54])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:seqio-index-getraw' on page 55 undefined on input
 line 948.


(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A2777BD02851C2FB632864165FCA4920
46548.pygtex) [55]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C6471BD02851C2FB632864165FCA4920
46548.pygtex) [56]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD73429543DFECA235A69AE23006BA05B
4EB70.pygtex [57])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4669566ECC2CFEDC7429F829576A
D0DC6.pygtex [58])

LaTeX Warning: Reference `sec:seqio-index-getraw' on page 59 undefined on input
 line 1189.


(./_minted-Tutorial/C194E2231D844AE7D0223173D2A899919543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEABD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqIO-fastq-conversion' on page 59 undefined on i
nput line 1232.


LaTeX Warning: Reference `sec:SeqIO-fasta-qual-conversion' on page 59 undefined
 on input line 1232.

[59]

LaTeX Warning: Reference `sec:seq-reverse-complement' on page 60 undefined on i
nput line 1247.


(./_minted-Tutorial/920133226A22EEB682D854077D7FB78FBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 60 undefine
d on input line 1258.


(./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C260028BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqIO-translate' on page 60 undefined on input li
ne 1311.

[60]
(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-format' on page 61 undefined on input l
ine 1331.


(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351
\OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) 
[]\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm
tt/m/n/10 SeqRecord.format(...)
[61]
(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397
[]\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm
tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt
/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:cookbook' on page 62 undefined on input line 
1412.


(./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B
4EB70.pygtex)) [62] (./Tutorial/chapter_align.tex
Chapter 6.

LaTeX Warning: Reference `sec:appendix-handles' on page 63 undefined on input l
ine 31.


LaTeX Warning: Reference `sec:AlignIO-count-argument' on page 63 undefined on i
nput line 35.


(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42669566ECC2CFEDC7429F829576A
D0DC6.pygtex [63])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AECBD02851C2FB632864165FCA4920
46548.pygtex [64])

LaTeX Warning: Reference `sec:alignment-format' on page 65 undefined on input l
ine 113.


(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A31077BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [65]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C560407BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533669566ECC2CFEDC7429F829576A
D0DC6.pygtex [66])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF756BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [67]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020669566ECC2CFEDC7429F829576A
D0DC6.pygtex [68])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [69]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D318BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477669566ECC2CFEDC7429F829576A
D0DC6.pygtex [70])
Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435
\OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t
or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()

LaTeX Warning: Reference `sec:SeqIO-conversion' on page 71 undefined on input l
ine 444.


Overfull \hbox (39.68698pt too wide) in paragraph at lines 442--447
[][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u
s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just
 use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert()

(./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F4024BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F669566ECC2CFEDC7429F829576A
D0DC6.pygtex [71])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99669566ECC2CFEDC7429F829576A
D0DC6.pygtex [72])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F169543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56669566ECC2CFEDC7429F829576A
D0DC6.pygtex [73])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE6BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-format' on page 74 undefined on input l
ine 633.


(./_minted-Tutorial/2590B11C695B984E246A0A91734F786CBD02851C2FB632864165FCA4920
46548.pygtex) [74]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE5BD02851C2FB632864165FCA4920
46548.pygtex [75])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B71692BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB00BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E59BD02851C2FB632864165FCA4920
46548.pygtex [76])

LaTeX Warning: Reference `sec:SeqRecord-addition' on page 77 undefined on input
 line 813.


(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A9253BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AE857C14E4731CC6F6EBA53051460097BD02851C2FB632864165FCA4920
46548.pygtex) [77]
(./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239CBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:subs_mat_ex' on page 78 undefined on input line 8
92.


(./_minted-Tutorial/523928538FA511A925EC995B1803BD16BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:pairwise' on page 78 undefined on input line 913.


[78]

LaTeX Warning: Reference `chapter:seqio' on page 79 undefined on input line 917
.


(./_minted-Tutorial/CD47D1913C82182C164BD47DA4715282BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:emboss-needle-water' on page 79 undefined on inpu
t line 947.


(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E893BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C63064BD02851C2FB632864165FCA4920
46548.pygtex) [79]
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A442BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F986368BD02851C2FB632864165FCA4920
46548.pygtex [80])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDFBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:phylo' on page 81 undefined on input line 109
3.


(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130
[]\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi
le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO

(./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BDBD02851C2FB632864165FCA4920
46548.pygtex [81])
(./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F739998BD02851C2FB632864165FCA4920
46548.pygtex [82])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E7454BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5CBD02851C2FB632864165FCA4920
46548.pygtex [83])
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE74BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:appendix-handles' on page 84 undefined on input l
ine 1317.


(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A240BD02851C2FB632864165FCA4920
46548.pygtex) [84]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/39152F199CEBB3375366F2E947824519BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF385674BD02851C2FB632864165FCA4920
46548.pygtex [85])
(./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE2493BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DF151703751D72BD556402B910190A87BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA88BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `durbin1998' on page 86 undefined on input line 1492.


(./_minted-Tutorial/554024580088332FAF0EA9296BACE82EBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:pairwise-aligner' on page 86 undefined on input l
ine 1505.

[86]
(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E361BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6CCC707502EDD92E9C355854215BF885BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C5BD02851C2FB632864165FCA4920
46548.pygtex [87])

LaTeX Warning: Citation `waterman1987' on page 88 undefined on input line 1578.



(./_minted-Tutorial/E5E00F47BD7A0C8BC5F8818526283868BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:pairwise-substitution-scores' on page 88 undefine
d on input line 1608.


LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 88 undefined o
n input line 1608.


LaTeX Warning: Reference `sec:pairwise-general-gapscores' on page 88 undefined 
on input line 1608.


LaTeX Warning: Reference `sec:pairwise-basic' on page 88 undefined on input lin
e 1609.


LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 88 undefined o
n input line 1612.


LaTeX Warning: Reference `sec:pairwise-general-gapscores' on page 88 undefined 
on input line 1613.


(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE04BD02851C2FB632864165FCA4920
46548.pygtex) [88]

LaTeX Warning: Citation `altschul1990' on page 89 undefined on input line 1639.



LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 89 undefined o
n input line 1639.


(./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD5BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `altschul1990' on page 89 undefined on input line 1668.



(./_minted-Tutorial/48453D528762FF183499778647AF218BBD02851C2FB632864165FCA4920
46548.pygtex [89])
(./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A39BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix
 []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu
tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt
t/m/n/10 aligner.mismatch_score

Overfull \hbox (47.73264pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat
rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t
ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt
/m/n/10 aligner.mismatch_score

LaTeX Warning: `h' float specifier changed to `ht'.


LaTeX Warning: Reference `table:align-meta-attributes' on page 90 undefined on 
input line 1772.


Overfull \hbox (32.852pt too wide) in paragraph at lines 1776--1820
[][]

(./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CEBD02851C2FB632864165FCA4920
46548.pygtex [90]) [91] [92]
(./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514ABD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:pairwise-examples' on page 93 undefined on input 
line 1908.

[93]
(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE1911BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB8671BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EFBD02851C2FB632864165FCA4920
46548.pygtex [94])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D01BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9FBD02851C2FB632864165FCA4920
46548.pygtex [95])
(./_minted-Tutorial/0758643069FF669538B9540ECD26C94CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A34296592BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/76E331C5187C259B69198E91FC4AD112BD02851C2FB632864165FCA4920
46548.pygtex [96])
(./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD357BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966BBD02851C2FB632864165FCA4920
46548.pygtex [97])
(./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/66AABFA387595237A8CE2518915213F8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B15E737F9393063B641148640673D991BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B46BD02851C2FB632864165FCA4920
46548.pygtex [98])
(./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/874975627BAB24A36A35FD4C633D246DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BDBD02851C2FB632864165FCA4920
46548.pygtex [99])
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A7BD02851C2FB632864165FCA4920
46548.pygtex [100])
(./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/52868B2F44504455E4969FEF2614B63BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB94BD02851C2FB632864165FCA4920
46548.pygtex) [101]
(./_minted-Tutorial/E7E68A8851DEEE300947A0531513417DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF65BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA1733BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `kent2002' on page 102 undefined on input line 2424.


(./_minted-Tutorial/6502BA65433924876427DBB6013C1003BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FDBD02851C2FB632864165FCA4920
46548.pygtex [102])
(./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F1012BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA5077BD02851C2FB632864165FCA4920
46548.pygtex [103])
(./_minted-Tutorial/779C61444C54C1736794F4E11B0E326DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E105BD02851C2FB632864165FCA4920
46548.pygtex [104])
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA77BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF796600BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613
\OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments 
is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing
 [][]\OT1/cmtt/m/n/10 len(alignments)

(./_minted-Tutorial/F89522EF58FB067C6521C367C7134716BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE20BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9CBD02851C2FB632864165FCA4920
46548.pygtex [105])
(./_minted-Tutorial/882BD2544386DECA236BF25C7DD64857BD02851C2FB632864165FCA4920
46548.pygtex [106])
(./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA70BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `schneider2005' on page 107 undefined on input line 272
5.


LaTeX Warning: Reference `sec:substitution_matrices' on page 107 undefined on i
nput line 2725.


(./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A29BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/13D646E6B49807044DBDC43707A09846BD02851C2FB632864165FCA4920
46548.pygtex [107])
(./_minted-Tutorial/467CA50C36874E405E988587FEC07686BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E62BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A94C18D2207C354646F831D57FD85B35BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D8BD02851C2FB632864165FCA4920
46548.pygtex [108])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A73BD02851C2FB632864165FCA4920
46548.pygtex [109])
(./_minted-Tutorial/AAF53200644F4F68779FB844730087D3BD02851C2FB632864165FCA4920
46548.pygtex [110])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE06BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057DBD02851C2FB632864165FCA4920
46548.pygtex [111])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/842D73F66680850822D006857AE71FE7BD02851C2FB632864165FCA4920
46548.pygtex) [112]
(./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE3135BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7C466424D72F09AE5AACA884161416F9BD02851C2FB632864165FCA4920
46548.pygtex [113])
(./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA825278BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F680093BD02851C2FB632864165FCA4920
46548.pygtex [114])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315ECBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D86241664707BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5669566ECC2CFEDC7429F829576A
D0DC6.pygtex [115])
(./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/60D893638743BD147116D13E00593D6CBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `altschul1990' on page 116 undefined on input line 3282
.


(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D669566ECC2CFEDC7429F829576A
D0DC6.pygtex [116])
(./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9EDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6DBD02851C2FB632864165FCA4920
46548.pygtex [117])

LaTeX Warning: Citation `henikoff1992' on page 118 undefined on input line 3354
.


LaTeX Warning: Citation `dayhoff1978' on page 118 undefined on input line 3354.



(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE9BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `schneider2005' on page 118 undefined on input line 337
9.


(./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F2519BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:pairwise' on page 118 undefined on input line 339
1.

(/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED0BD02851C2FB632864165FCA4920
46548.pygtex) [118]
(./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F120EF3444F3192D48657B4E52407017BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F2091BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5DBD02851C2FB632864165FCA4920
46548.pygtex [119])
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C71BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75ABD02851C2FB632864165FCA4920
46548.pygtex [120])) [121] (./Tutorial/chapter_blast.tex
Chapter 7.

LaTeX Warning: Reference `chapter:searchio' on page 122 undefined on input line
 18.


Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46
[]\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas
t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs 
&
[122]
(./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB1BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:parsing-blast' on page 123 undefined on input lin
e 73.


(./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4EBD02851C2FB632864165FCA4920
46548.pygtex [123])

LaTeX Warning: Reference `chapter:seqio' on page 124 undefined on input line 13
3.


LaTeX Warning: Reference `sec:parsing-blast' on page 124 undefined on input lin
e 138.


(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC6BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:parsing-blast' on page 124 undefined on input lin
e 160.


(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:parsing-blast' on page 124 undefined on input lin
e 169.


LaTeX Warning: Reference `sec:running-www-blast' on page 124 undefined on input
 line 178.

[124]

LaTeX Warning: Reference `sec:alignment-tools' on page 125 undefined on input l
ine 206.


(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE4792BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:parsing-blast' on page 125 undefined on input lin
e 241.

[125]

LaTeX Warning: Reference `sec:running-www-blast' on page 126 undefined on input
 line 287.


LaTeX Warning: Reference `sec:running-local-blast' on page 126 undefined on inp
ut line 289.


LaTeX Warning: Reference `sec:appendix-handles' on page 126 undefined on input 
line 304.


(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE5218004BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 126 undefined on input line 34
0.


LaTeX Warning: Reference `chapter:align' on page 126 undefined on input line 34
0.


(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F40394BD02851C2FB632864165FCA4920
46548.pygtex [126])
(./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D238BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68259DF5B1930070C029D5A72D891A36BD02851C2FB632864165FCA4920
46548.pygtex [127])
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924669566ECC2CFEDC7429F829576A
D0DC6.pygtex)

LaTeX Warning: Reference `fig:blastrecord' on page 128 undefined on input line 
452.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:psiblastrecord' on page 128 undefined on input li
ne 468.

Excluding 'htmlonly' comment.

LaTeX Warning: Float too large for page by 32.27644pt on input line 481.

) [128] [129 <./images/BlastRecord.png>] [130 <./images/PSIBlastRecord.png>]
(./Tutorial/chapter_searchio.tex
Chapter 8.

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [131]
Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93
[][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle 
con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10
 HSPFragment

Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107
[][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files
 with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/
m/n/10 QueryResult

(./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FCBD02851C2FB632864165FCA4920
46548.pygtex [132])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B51955BD02851C2FB632864165FCA4920
46548.pygtex [133])
(./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/362861C831165FEA5413E0240053CD89BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE327BD02851C2FB632864165FCA4920
46548.pygtex [134])
(./_minted-Tutorial/FD9C81C098491598DBFB6208173BB575BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A03BD02851C2FB632864165FCA4920
46548.pygtex) [135]
(./_minted-Tutorial/0B914838010D3E86EC368E1702EB7253BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E619BD02851C2FB632864165FCA4920
46548.pygtex [136])
(./_minted-Tutorial/DDECA9EB99D9FA38003A52C176593072BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/578CBF904F35965EECFEC1FA694F0752BD02851C2FB632864165FCA4920
46548.pygtex [137])
(./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD64BD02851C2FB632864165FCA4920
46548.pygtex) [138]
(./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC6246863BD02851C2FB632864165FCA4920
46548.pygtex) [139]
(./_minted-Tutorial/A3385B945E43CC076FFA693B27681F05BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE573577BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B46BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD95BD02851C2FB632864165FCA4920
46548.pygtex [140])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD880444BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C787BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:seq_annot' on page 141 undefined on input lin
e 739.


Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745
[]\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10
 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr
/m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment

(./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920
46548.pygtex [141])
(./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920
46548.pygtex [142])
(./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920
46548.pygtex [143])
(./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920
46548.pygtex) [144]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059
\OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT
1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like 
[][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F4BD02851C2FB632864165FCA4920
46548.pygtex) [145]

LaTeX Warning: Reference `sec:SeqIO-index' on page 146 undefined on input line 
1089.


Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092
[]\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us
-ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt
/m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E9868BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE55BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DEBD02851C2FB632864165FCA4920
46548.pygtex) [146]
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170
[]\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 
also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic
h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse

(./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C176BD02851C2FB632864165FCA4920
46548.pygtex)) [147] (./Tutorial/chapter_entrez.tex
Chapter 9.
[148]

LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 149 undefined
 on input line 21.


(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB5BD02851C2FB632864165FCA4920
46548.pygtex) [149]

LaTeX Warning: Reference `sec:entrez-webenv' on page 150 undefined on input lin
e 60.


LaTeX Warning: Reference `sec:BioSQL' on page 150 undefined on input line 63.


(./_minted-Tutorial/7692669934D8ED6DEE1B8B6684745421BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA36BD02851C2FB632864165FCA4920
46548.pygtex [150])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C008BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FACBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F6BD02851C2FB632864165FCA4920
46548.pygtex [151])
(./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C68BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:efetch' on page 152 undefined on input line 216.


LaTeX Warning: Reference `sec:entrez-einfo' on page 152 undefined on input line
 220.


(./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D50277BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:efetch' on page 152 undefined on input line 236.

[152]
(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19FBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 153 undefined on input lin
e 299.

[153]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE4BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 154 undefined on in
put line 325.


LaTeX Warning: Reference `sec:efetch' on page 154 undefined on input line 325.


(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F3147BD02851C2FB632864165FCA4920
46548.pygtex [154] [155])

LaTeX Warning: Reference `chapter:seqio' on page 156 undefined on input line 41
9.


(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D59543DFECA235A69AE23006BA05B
4EB70.pygtex [156])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F487BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 157 undefined
 on input line 481.


LaTeX Warning: Reference `sec:entrez-webenv' on page 157 undefined on input lin
e 483.


(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF008BD02851C2FB632864165FCA4920
46548.pygtex [157])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68622353B578A611D2F621023E3C4BD1BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:elink-citations' on page 158 undefined on input l
ine 565.


LaTeX Warning: Reference `sec:entrez_example_genbank' on page 158 undefined on 
input line 571.


(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F70BD02851C2FB632864165FCA4920
46548.pygtex [158])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC38BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0944BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722ABD02851C2FB632864165FCA4920
46548.pygtex [159])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF38669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0BBD02851C2FB632864165FCA4920
46548.pygtex [160])
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B669566ECC2CFEDC7429F829576A
D0DC6.pygtex [161])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6EF35C66998219AA15568E5FA366261EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD3676C48A9629929A55320028B512E5BD02851C2FB632864165FCA4920
46548.pygtex [162])

LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 163 undefined on in
put line 818.


LaTeX Warning: Reference `sec:efetch' on page 163 undefined on input line 818.


(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD669566ECC2CFEDC7429F829576A
D0DC6.pygtex [163])
(./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC12BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D75BD02851C2FB632864165FCA4920
46548.pygtex [164])
(./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E277BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 165 undefined on input lin
e 940.


(./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A1266BD02851C2FB632864165FCA4920
46548.pygtex [165])
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019669566ECC2CFEDC7429F829576A
D0DC6.pygtex [166])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B624BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA5BD02851C2FB632864165FCA4920
46548.pygtex) [167]
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA19543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 168 undefined on input line 1110
.


(./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1EBD02851C2FB632864165FCA4920
46548.pygtex [168])

LaTeX Warning: Reference `sec:entrez-webenv' on page 169 undefined on input lin
e 1153.


(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD0BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 169 undefined on input line 1199
.


(./_minted-Tutorial/964257041BEB9E732FF9A943209BD6EDBD02851C2FB632864165FCA4920
46548.pygtex [169])
(./_minted-Tutorial/600193D5D5D44162E61A3CAB40448426BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B642038BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A0BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 170 undefined on input lin
e 1254.


(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A1BD02851C2FB632864165FCA4920
46548.pygtex [170])

LaTeX Warning: Reference `sec:entrez-webenv' on page 171 undefined on input lin
e 1289.


LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 171 undefined on in
put line 1296.


LaTeX Warning: Reference `sec:entrez-webenv' on page 171 undefined on input lin
e 1297.


(./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FDBD02851C2FB632864165FCA4920
46548.pygtex [171])
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A72797BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB3848BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 172 undefined on input line 13
49.


(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D76169664531538D144C55FFC33571BBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:entrez-guidelines' on page 172 undefined on input
 line 1373.


LaTeX Warning: Reference `sec:entrez-webenv' on page 172 undefined on input lin
e 1374.

[172]
(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C45BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB93649BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D8BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:entrez-search-fetch-genbank' on page 173 undefine
d on input line 1434.

[173]
(./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C477BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:entrez_example_genbank' on page 174 undefined on 
input line 1456.


(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E24BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F9633BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D5749543DFECA235A69AE23006BA05B
4EB70.pygtex [174])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA9543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:entrez-and-medline' on page 175 undefined on inpu
t line 1545.


LaTeX Warning: Reference `sec:elink' on page 175 undefined on input line 1550.

[175]
(./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB2BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 176 undefined on input lin
e 1575.


(./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927ABD02851C2FB632864165FCA4920
46548.pygtex)) [176] (./Tutorial/chapter_uniprot.tex
Chapter 10.

LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 177 undefined
 on input line 12.


(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A86BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A668BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD6768BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:expasy_swissprot' on page 177 undefined on input 
line 37.


(./_minted-Tutorial/930B60BD569CAAF368B0E614553F3030BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 177 undefined
 on input line 45.

[177]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA6519182BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB934669BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD69228BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D14BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C06BD02851C2FB632864165FCA4920
46548.pygtex [178])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A4517918BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09ABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224669566ECC2CFEDC7429F829576A
D0DC6.pygtex [179])
(./_minted-Tutorial/956383F4066B9E093C9D2E3843CA0220BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307BBD02851C2FB632864165FCA4920
46548.pygtex [180])
(./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E2BD02851C2FB632864165FCA4920
46548.pygtex) [181]
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC783BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF9BD02851C2FB632864165FCA4920
46548.pygtex [182])
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B4BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 183 undefined on input line 345.



(./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B622BD02851C2FB632864165FCA4920
46548.pygtex [183])
Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366
[]\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n
/10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/
m/n/10 SwissProt.read(handle)

(./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87DBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410
[]\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m
en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re
cord

(./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B753BD02851C2FB632864165FCA4920
46548.pygtex) [184]
(./_minted-Tutorial/9457A436D281E066D350873A88476E59BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E7BD02851C2FB632864165FCA4920
46548.pygtex [185])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E86169BD02851C2FB632864165FCA4920
46548.pygtex)) [186] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C22853BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E69085BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C71BD02851C2FB632864165FCA4920
46548.pygtex [187])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA7388BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB35BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB8231BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:problem_structures' on page 188 undefined on inpu
t line 84.


(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879EBD02851C2FB632864165FCA4920
46548.pygtex) [188]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E18BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D176BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A024BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A5BD02851C2FB632864165FCA4920
46548.pygtex) [189]
(./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB136BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECECBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA4BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264
\OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m
/n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato
m)
[190]

LaTeX Warning: Reference `fig:smcra' on page 191 undefined on input line 275.


LaTeX Warning: Reference `sec:problem_structures' on page 191 undefined on inpu
t line 284.

Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D979BD02851C2FB632864165FCA4920
46548.pygtex) [191] [192 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD855BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB247BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E2727622BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A12BD02851C2FB632864165FCA4920
46548.pygtex) [193]

LaTeX Warning: Reference `sec:hetero_problems' on page 194 undefined on input l
ine 421.


(./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E3BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:point_mutations' on page 194 undefined on input l
ine 466.


(./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DCBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:disordered_atoms' on page 194 undefined on input 
line 483.

[194]
(./_minted-Tutorial/35E34E333445AAAA4E33570211335BA5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B1BD02851C2FB632864165FCA4920
46548.pygtex [195])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC88098BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB12492BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `fig:smcra' on page 196 undefined on input line 610.


(./_minted-Tutorial/76657140082404C594EE786B642215C3BD02851C2FB632864165FCA4920
46548.pygtex [196])

LaTeX Warning: Reference `fig:smcra' on page 197 undefined on input line 657.


(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254CBD02851C2FB632864165FCA4920
46548.pygtex) [197]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB90BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B128BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B3BD02851C2FB632864165FCA4920
46548.pygtex [198])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF231899BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A624BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC2663BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA39BD02851C2FB632864165FCA4920
46548.pygtex [199])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E667BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899BBD02851C2FB632864165FCA4920
46548.pygtex [200])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AE729029ED6ABA2E38F17FAA1C60732CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8BB12A44CF293B1BF656E236EFE0BE12BD02851C2FB632864165FCA4920
46548.pygtex [201])
(./_minted-Tutorial/F0EFB999D116D041397B95C62B2EED29BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FE5531F727D4D28736FC18DF8A430EBBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E045C9432637E8C515E37CB4917FD57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AD9DB5C434FCB2537E43EF340112BD08BD02851C2FB632864165FCA4920
46548.pygtex [202])
(./_minted-Tutorial/C1D5880B46A9CAEDCEB7F545F21B98CBBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (4.2397pt too wide) in paragraph at lines 1070--1074
\OT1/cmr/m/n/10 Missing atoms and other is-sues can cause prob-lems when re-bui
ld-ing a struc-ture. Use \OT1/cmtt/m/n/10 structure[]rebuild[]test$$

(./_minted-Tutorial/BD4323A41DFED2A7E4CD261AA65F95EDBD02851C2FB632864165FCA4920
46548.pygtex) [203]
(./_minted-Tutorial/6395F38A139598C6CC297CDBA73A8A43BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/21D2C13C2AA9395E0B1E4F1DDC801798BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/12E711A2CBFD0B046AA026208A117C1E9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/813FE78A3F8D8E46F06FF71539F000E69543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/CD78F368EB103F71947A3184BB62B46F9543DFECA235A69AE23006BA05B
4EB70.pygtex [204])
(./_minted-Tutorial/8E34478E945971E05C77F0A0E8C1B9D89543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/0D3FBB23D21A6A468370D56058193010BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BBA5405CCC4A3178ADA49DA358246C819543DFECA235A69AE23006BA05B
4EB70.pygtex [205])
(./_minted-Tutorial/DE601B1883F045FBEE1B28168CFF0CCABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AAF43F15691D49893FAEEAB7B7693A1D9543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `fig:distanceplot' on page 206 undefined on input line
 1261.


(./_minted-Tutorial/0ABBC5325B76EBCC5687BB33E7595F219543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment. [206 <./images/1a8o-ca-plot.png>]
Overfull \hbox (15.27203pt too wide) in paragraph at lines 1292--1295
[]\OT1/cmr/m/n/10 This work uses equa-tions de-vel-oped by Blue, the Hedronome-
ter, dis-cussed in [][]$\OT1/cmtt/m/n/10 https : / / math . stackexchange .

Overfull \hbox (116.15723pt too wide) in paragraph at lines 1292--1295
\OT1/cmtt/m/n/10 com / a / 49340 / 409$[][] \OT1/cmr/m/n/10 and fur-ther in [][
]$\OT1/cmtt/m/n/10 http : / / daylateanddollarshort . com / mathdocs / Heron-[]
like-[]Results-[]for-[]Tetrahedral-[]Volume .

(./_minted-Tutorial/BACD9263B6DB9FE9B9C8FA59C017D190BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2AECB4AED1E5DFDC387B42EF509CC3F4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1D3E5D8C6C6880A4C1D7DC0DEE7DC0C7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/815743EBD76EB14B6A71E1A4AE6433A4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B285099D410967E19F3165C7B5395544BD02851C2FB632864165FCA4920
46548.pygtex [207])

LaTeX Warning: Reference `fig:phepairs' on page 208 undefined on input line 138
3.

Excluding 'htmlonly' comment.
(./_minted-Tutorial/5DFAFA7DE84292336F50FFB5DD8AD22A9543DFECA235A69AE23006BA05B
4EB70.pygtex [208 <./images/phe-pairs-3pbl.png>])
(./_minted-Tutorial/ED5201F27B6F2CC7A881AC419DF87B5E9543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `table:ic-attribs' on page 209 undefined on input line
 1455.


Overfull \hbox (214.06847pt too wide) in paragraph at lines 1458--1474
[][] 
[209]

LaTeX Warning: Citation `golub1989' on page 210 undefined on input line 1496.


(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993CBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `hamelryck2005' on page 210 undefined on input line 152
4.


LaTeX Warning: Command \r invalid in math mode on input line 1527.


(./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705EBD02851C2FB632864165FCA4920
46548.pygtex [210])

LaTeX Warning: Reference `table:DSSP-codes' on page 211 undefined on input line
 1559.


LaTeX Warning: Reference `sec:residue_depth' on page 211 undefined on input lin
e 1599.


(./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C6709BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/895E3343902EFB0E5475667B01C4B691BD02851C2FB632864165FCA4920
46548.pygtex [211])

LaTeX Warning: Citation `hamelryck2003a' on page 212 undefined on input line 16
50.

[212]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB15BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A9BD02851C2FB632864165FCA4920
46548.pygtex [213])
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A74BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5DBD02851C2FB632864165FCA4920
46548.pygtex) [214]

LaTeX Warning: Citation `hamelryck2003b' on page 215 undefined on input line 18
61.


LaTeX Warning: Citation `majumdar2005' on page 215 undefined on input line 1862
.

) [215] (./Tutorial/chapter_popgen.tex
Chapter 12.

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6B9543DFECA235A69AE23006BA05B
4EB70.pygtex) [216]
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC9543DFECA235A69AE23006BA05B
4EB70.pygtex)) [217] (./Tutorial/chapter_phylo.tex
Chapter 13.

LaTeX Warning: Citation `talevich2012' on page 218 undefined on input line 9.


(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15844BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C24BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4ADBD02851C2FB632864165FCA4920
46548.pygtex [218])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DDBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `fig:phylo-simple-draw' on page 219 undefined on input
 line 96.


(./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920
46548.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBABD02851C2FB632864165FCA4920
46548.pygtex) [219]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1ADBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185
[]\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t
he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor

(./_minted-Tutorial/29624A9666C9430AABADF395148BBF27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972DBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `fig:phylo-color-draw' on page 220 undefined on input 
line 201.


(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920
46548.pygtex [220 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9BBD02851C2FB632864165FCA4920
46548.pygtex [221 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/456F5679DCD4FF740E7A110889D86573BD02851C2FB632864165FCA4920
46548.pygtex [222])
(./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F55BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D3BD02851C2FB632864165FCA4920
46548.pygtex [223])
(./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEEBD02851C2FB632864165FCA4920
46548.pygtex) Excluding 'htmlonly' comment. [224 <./images/phylo-draw-example.p
ng>]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486
\OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, 
[][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"})
[225]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537
[]\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, 
find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10
 ,
[226]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B
4EB70.pygtex) [227]
Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707
[]\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter
-act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier .

(./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD8119BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095BBD02851C2FB632864165FCA4920
46548.pygtex) [228]
(./_minted-Tutorial/0702C9875263768417DD3ED2EF78755EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D2BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:PhyloXML' on page 229 undefined on input line 823
.

[229]) [230] (./Tutorial/chapter_motifs.tex
Chapter 14.

LaTeX Warning: Reference `sec:links' on page 231 undefined on input line 8.


(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486ABD02851C2FB632864165FCA4920
46548.pygtex [231])
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D03BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE75BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D177BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D257173BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/86717C2BCE65F41FCDB8652763165857BD02851C2FB632864165FCA4920
46548.pygtex [232])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F61243192022BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `cornish1985' on page 233 undefined on input line 165.


LaTeX Warning: Citation `cavener1987' on page 233 undefined on input line 166.


(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB2476BD02851C2FB632864165FCA4920
46548.pygtex) [233]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA669566ECC2CFEDC7429F829576A
D0DC6.pygtex [234])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECDBD02851C2FB632864165FCA4920
46548.pygtex [235])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C76BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92669566ECC2CFEDC7429F829576A
D0DC6.pygtex [236])
(./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F706BD02851C2FB632864165FCA4920
46548.pygtex [237])
(./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DCBD02851C2FB632864165FCA4920
46548.pygtex [238])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFDBD02851C2FB632864165FCA4920
46548.pygtex [239])
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C378BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6BBD02851C2FB632864165FCA4920
46548.pygtex [240])

LaTeX Warning: Citation `bailey1994' on page 241 undefined on input line 542.


(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44669566ECC2CFEDC7429F829576A
D0DC6.pygtex [241])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909FBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606
\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man
d reads the com-plete file di-rectly, so you can close the file af-ter call-ing
 [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B84BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB6BD02851C2FB632864165FCA4920
46548.pygtex [242])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E012053BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `matys2003' on page 243 undefined on input line 688.


(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7669566ECC2CFEDC7429F829576A
D0DC6.pygtex [243])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5CBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `table:transfaccodes' on page 244 undefined on input l
ine 772.


LaTeX Warning: `h' float specifier changed to `ht'.

[244]
(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EFBD02851C2FB632864165FCA4920
46548.pygtex [245])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F26406BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF51495BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE70605BD02851C2FB632864165FCA4920
46548.pygtex [246])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C74BD02851C2FB632864165FCA4920
46548.pygtex [247])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C98812BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E225BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E48BD02851C2FB632864165FCA4920
46548.pygtex [248])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7BBD02851C2FB632864165FCA4920
46548.pygtex [249])
(./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A81BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA161BD02851C2FB632864165FCA4920
46548.pygtex) [250]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E25BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A5092BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C86073BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE970BD02851C2FB632864165FCA4920
46548.pygtex [251])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF4BD02851C2FB632864165FCA4920
46548.pygtex [252])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E322BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD7261603BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA2473BD02851C2FB632864165FCA4920
46548.pygtex [253])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA16BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D3BD02851C2FB632864165FCA4920
46548.pygtex) [254]
(./_minted-Tutorial/868ABF9ABD2736A12F423306646D7706BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/912C817861E626118AB2FA06F12910B6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A26BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [255]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB41BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B6BD02851C2FB632864165FCA4920
46548.pygtex) [256]) [257] (./Tutorial/chapter_cluster.tex
Chapter 15.

LaTeX Warning: Citation `dehoon2004' on page 258 undefined on input line 6.


LaTeX Warning: Citation `lecuyer1988' on page 258 undefined on input line 30.


LaTeX Warning: Citation `kachitvichyanukul1988' on page 258 undefined on input 
line 30.

[258] [259] [260]

LaTeX Warning: Citation `snedecor1989' on page 261 undefined on input line 154.


[261]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 262 undefined on input
 line 183.


(./_minted-Tutorial/C2B72A7408C7DF74DFCEBE0485997287BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE601735827BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A25009543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C0BD02851C2FB632864165FCA4920
46548.pygtex [262])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246
\OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra
nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$

(./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB34BD02851C2FB632864165FCA4920
46548.pygtex) [263]

LaTeX Warning: Reference `sec:distancefunctions' on page 264 undefined on input
 line 278.

[264]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762EBD02851C2FB632864165FCA4920
46548.pygtex) [265]

LaTeX Warning: Reference `sec:distancefunctions' on page 266 undefined on input
 line 346.


(./_minted-Tutorial/C286E2777B917B774560CBDC7CF92626BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B
4EB70.pygtex) [266] [267]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424
[][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them.
 The items be-ing clus-tered are num-bered from 0 to $[]$,

(./_minted-Tutorial/015798D317E9D8732518AFD186C997CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C239049267861739BD02851C2FB632864165FCA4920
46548.pygtex) [268]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE22BD02851C2FB632864165FCA4920
46548.pygtex) [269]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F72BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D41BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF8895055BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 270 undefined on input
 line 556.


(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEBBD02851C2FB632864165FCA4920
46548.pygtex [270])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Citation `kohonen1997' on page 271 undefined on input line 600.


LaTeX Warning: Citation `tamayo1999' on page 271 undefined on input line 600.

[271]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C175BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 272 undefined on input
 line 647.

[272]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

LaTeX Warning: Citation `yeung2001' on page 273 undefined on input line 660.


LaTeX Warning: Citation `golub1971' on page 273 undefined on input line 668.


(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEABD02851C2FB632864165FCA4920
46548.pygtex) [273]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961CBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750
 [] 
[274] [275]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F7BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 276 undefined on input
 line 802.


LaTeX Warning: Reference `sec:distancematrix' on page 276 undefined on input li
ne 805.


(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAFBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:clustercentroids' on page 276 undefined on input 
line 823.


(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FCBD02851C2FB632864165FCA4920
46548.pygtex) [276]

LaTeX Warning: Reference `sec:distancefunctions' on page 277 undefined on input
 line 846.


(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241DBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 277 undefined on input
 line 871.


(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E0BD02851C2FB632864165FCA4920
46548.pygtex [277])

LaTeX Warning: Reference `sec:distancefunctions' on page 278 undefined on input
 line 900.


(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA8504BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 278 undefined on input
 line 922.

[278]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C4BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Citation `hihara2001' on page 279 undefined on input line 954.


(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D70BD02851C2FB632864165FCA4920
46548.pygtex [279])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF58BD02851C2FB632864165FCA4920
46548.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116
[]\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result
_K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT
1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 
. 
[280] (./Tutorial/chapter_learning.tex
Chapter 16.
[281]

LaTeX Warning: Reference `eq:OP' on page 282 undefined on input line 40.


LaTeX Warning: Reference `eq:NOP' on page 282 undefined on input line 40.


LaTeX Warning: Reference `table:training' on page 282 undefined on input line 7
5.


(./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4DBD02851C2FB632864165FCA4920
46548.pygtex [282])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4FBD02851C2FB632864165FCA4920
46548.pygtex [283])
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB096BD02851C2FB632864165FCA4920
46548.pygtex [284])

LaTeX Warning: Reference `eq:OP' on page 285 undefined on input line 197.


LaTeX Warning: Reference `eq:NOP' on page 285 undefined on input line 197.


(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D402BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A012BD02851C2FB632864165FCA4920
46548.pygtex [285])

LaTeX Warning: Reference `eq:OP' on page 286 undefined on input line 261.


LaTeX Warning: Reference `eq:NOP' on page 286 undefined on input line 261.


LaTeX Warning: Reference `eq:OP' on page 286 undefined on input line 263.


LaTeX Warning: Reference `eq:NOP' on page 286 undefined on input line 263.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 267.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 267.


LaTeX Warning: Reference `sec:LogisticRegression' on page 286 undefined on inpu
t line 273.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 275.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 275.


LaTeX Warning: Reference `table:training' on page 286 undefined on input line 2
77.


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E6BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:LogisticRegressionTraining' on page 286 undefined
 on input line 285.

[286]

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 287.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 287.


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA595BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B38BF6A3D910590D450B331A075B723CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC1BD02851C2FB632864165FCA4920
46548.pygtex [287])
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC15BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A586FFDD9483C890754DBE5DFC420710BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D35BD02851C2FB632864165FCA4920
46548.pygtex [288])) [289] (./Tutorial/chapter_graphics.tex
Chapter 17.

LaTeX Warning: Citation `pritchard2006' on page 290 undefined on input line 18.



LaTeX Warning: Citation `toth2006' on page 290 undefined on input line 28.


LaTeX Warning: Citation `vanderauwera2009' on page 290 undefined on input line 
31.


LaTeX Warning: Reference `chapter:seq_annot' on page 290 undefined on input lin
e 36.


LaTeX Warning: Reference `chapter:seqio' on page 290 undefined on input line 36
.

[290]

LaTeX Warning: Reference `chapter:seqio' on page 291 undefined on input line 64
.


(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A09543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D8169543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B0359543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_linear' on page 291 undefined on input li
ne 136.


(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA79543DFECA235A69AE23006BA05B
4EB70.pygtex [291]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_circular' on page 292 undefined on input 
line 167.


(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E9543DFECA235A69AE23006BA05B
4EB70.pygtex [292 <./images/plasmid_linear.png (PNG copy)>])

LaTeX Warning: Reference `sec:seq_features' on page 293 undefined on input line
 220.

[293 <./images/plasmid_circular.png (PNG copy)>]
(./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF279543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A7359543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_labels' on page 294 undefined on input l
ine 260.


(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D8509543DFECA235A69AE23006BA05B
4EB70.pygtex [294]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_labels' on page 295 undefined on input l
ine 330.


LaTeX Warning: Reference `sec:gd_features_without_seqfeatures' on page 295 unde
fined on input line 339.


LaTeX Warning: Reference `sec:gd_feature_captions' on page 295 undefined on inp
ut line 339.


LaTeX Warning: Reference `sec:gd_features_without_seqfeatures' on page 295 unde
fined on input line 339.


LaTeX Warning: Reference `sec:gd_feature_captions' on page 295 undefined on inp
ut line 339.


LaTeX Warning: Reference `sec:gd_nice_example' on page 295 undefined on input l
ine 345.


(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B949543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C9543DFECA235A69AE23006BA05B
4EB70.pygtex [295] [296 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigils' on page 297 undefined on input line 38
7.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `sec:gd_sigils' on page 297 undefined on input line 40
3.


(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_arrow_shafts' on page 297 undefined on i
nput line 434.


LaTeX Warning: Reference `sec:gd_arrow_sigils' on page 297 undefined on input l
ine 439.


(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_arrow_heads' on page 297 undefined on in
put line 463.


LaTeX Warning: Reference `sec:gd_arrow_sigils' on page 297 undefined on input l
ine 468.


(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F9543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:gd_top_down' on page 297 undefined on input line 
488.


(./_minted-Tutorial/67B3F646AA5F8690151428081229D39B9543DFECA235A69AE23006BA05B
4EB70.pygtex [297] [298 <./images/GD_sigils.png>] [299 <./images/GD_sigil_arrow
_shafts.png>] [300 <./images/GD_sigil_arrow_heads.png>] [301])
Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_linear_nice' on page 302 undefined on inp
ut line 570.


LaTeX Warning: Reference `fig:plasmid_circular_nice' on page 302 undefined on i
nput line 571.


LaTeX Warning: Reference `sec:gd_nice_example' on page 302 undefined on input l
ine 577.


LaTeX Warning: Reference `sec:gd_nice_example' on page 302 undefined on input l
ine 577.


LaTeX Warning: Reference `sec:gd_nice_example' on page 302 undefined on input l
ine 585.


LaTeX Warning: Reference `sec:gd_nice_example' on page 302 undefined on input l
ine 585.


LaTeX Warning: Citation `proux2002' on page 302 undefined on input line 596.


LaTeX Warning: Reference `sec:efetch' on page 302 undefined on input line 605.


LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 302 undefined on input
 line 608.


LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 302 undefin
ed on input line 610.

[302 <./images/plasmid_linear_nice.png (PNG copy)>] [303 <./images/plasmid_circ
ular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA899543DFECA235A69AE23006BA05B
4EB70.pygtex [304])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177A9543DFECA235A69AE23006BA05B
4EB70.pygtex [305]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:three_track_simple' on page 306 undefined on inpu
t line 732.


LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 306 undefined on inpu
t line 739.


LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 306 undefined on inpu
t line 739.


LaTeX Warning: Citation `proux2002' on page 306 undefined on input line 759.


(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA1119543DFECA235A69AE23006BA05B
4EB70.pygtex [306 <./images/three_track_simple.png>])
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD18409543DFECA235A69AE23006BA05B
4EB70.pygtex [307])
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C289543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879
[]\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the
 [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm
tt/m/n/10 cross_track_links
Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:three_track_cl' on page 308 undefined on input li
ne 894.


LaTeX Warning: Reference `sec:gd_cross_links' on page 308 undefined on input li
ne 901.


LaTeX Warning: Reference `sec:gd_cross_links' on page 308 undefined on input li
ne 901.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:three_track_cl2' on page 308 undefined on input l
ine 927.


LaTeX Warning: Reference `sec:gd_cross_links' on page 308 undefined on input li
ne 934.


LaTeX Warning: Reference `sec:gd_cross_links' on page 308 undefined on input li
ne 934.

[308] [309 <./images/three_track_cl.png>] [310 <./images/three_track_cl2a.png>]

(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F7284149779543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F9543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Citation `jupe2012' on page 311 undefined on input line 1012.


(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC9543DFECA235A69AE23006BA05B
4EB70.pygtex [311] [312 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])

(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C9543DFECA235A69AE23006BA05B
4EB70.pygtex [313]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:simplechromosome' on page 314 undefined on input 
line 1114.


(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A759543DFECA235A69AE23006BA05B
4EB70.pygtex [314]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:simplechromosome' on page 315 undefined on input 
line 1194.

) [315] (./Tutorial/chapter_kegg.tex
Chapter 18.

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C71BD02851C2FB632864165FCA4920
46548.pygtex) [316]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B9543DFECA235A69AE23006BA05B
4EB70.pygtex [317])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95669566ECC2CFEDC7429F829576A
D0DC6.pygtex)) [318] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8DBD02851C2FB632864165FCA4920
46548.pygtex) [319]
(./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA9721BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB44BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB081BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF8BD02851C2FB632864165FCA4920
46548.pygtex [320])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D7206BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579DBD02851C2FB632864165FCA4920
46548.pygtex [321])
(./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E0872188BD02851C2FB632864165FCA4920
46548.pygtex [322])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E6BD02851C2FB632864165FCA4920
46548.pygtex)) [323] (./Tutorial/chapter_cookbook.tex
Chapter 20.

LaTeX Warning: Reference `chapter:seqio' on page 324 undefined on input line 22
.


(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB9543DFECA235A69AE23006BA05B
4EB70.pygtex [324])

LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 325 undefined on i
nput line 58.


(./_minted-Tutorial/CA0835D76EF6887731674D8AB555091B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E57164BD02851C2FB632864165FCA4920
46548.pygtex) [325]
(./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD4BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 326 undefined on 
input line 146.


(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54F9543DFECA235A69AE23006BA05B
4EB70.pygtex [326])

LaTeX Warning: Reference `sec:translation' on page 327 undefined on input line 
201.


LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 327 undefined o
n input line 206.


(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F649543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A02396470619543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B9543DFECA235A69AE23006BA05B
4EB70.pygtex [327])
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC655419543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE4087939543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:seqio-index-getraw' on page 328 undefined on inpu
t line 338.

[328]
(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA29543DFECA235A69AE23006BA05B
4EB70.pygtex) [329]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF6418319543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F354509543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 330 undefined on i
nput line 443.


LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 330 undefined on i
nput line 457.


Overfull \hbox (5.83499pt too wide) in paragraph at lines 454--458
\OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul
d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B
4EB70.pygtex [330])
Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477
\OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849.
fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[
]primer.fastq\OT1/cmr/m/n/10 . 

LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 331 undefined on input
 line 480.


(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA5569543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A9543DFECA235A69AE23006BA05B
4EB70.pygtex [331])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C9543DFECA235A69AE23006BA05B
4EB70.pygtex) [332]
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F89159543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:SeqIO-conversion' on page 333 undefined on input 
line 643.


LaTeX Warning: Citation `cock2010' on page 333 undefined on input line 646.

[333]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C319543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC407373679543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D2587BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B69543DFECA235A69AE23006BA05B
4EB70.pygtex [334])
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A09543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:SeqIO-index' on page 335 undefined on input line 
801.


(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582EBD02851C2FB632864165FCA4920
46548.pygtex [335])

LaTeX Warning: Reference `sec:SeqIO-index' on page 336 undefined on input line 
823.


LaTeX Warning: Reference `sec:SeqIO-sort' on page 336 undefined on input line 8
25.


LaTeX Warning: Reference `sec:SeqIO-conversion' on page 336 undefined on input 
line 839.


(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7DBD02851C2FB632864165FCA4920
46548.pygtex [336])

LaTeX Warning: Reference `sec:translation' on page 337 undefined on input line 
905.


(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF098BD02851C2FB632864165FCA4920
46548.pygtex) [337]
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052669566ECC2CFEDC7429F829576A
D0DC6.pygtex [338])

LaTeX Warning: Reference `sec:gd_nice_example' on page 339 undefined on input l
ine 1024.


LaTeX Warning: Reference `chapter:seqio' on page 339 undefined on input line 10
41.


(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B79543DFECA235A69AE23006BA05B
4EB70.pygtex [339]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:seq-len-hist' on page 340 undefined on input line
 1109.


Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120
[]\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10
 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use
 [][]\OT1/cmtt/m/n/10 pylab.savefig(...)

(./_minted-Tutorial/798776F436EA559BACD9C305C09973919543DFECA235A69AE23006BA05B
4EB70.pygtex [340 <./images/hist_plot.png>])
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:seq-gc-plot' on page 341 undefined on input line 
1177.


LaTeX Warning: Reference `fig:nuc-dot-plot' on page 341 undefined on input line
 1191.

Excluding 'htmlonly' comment. [341 <./images/gc_plot.png>]
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF79543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/80A47C8780CE3021D53829563E8166569543DFECA235A69AE23006BA05B
4EB70.pygtex [342 <./images/dot_plot.png>])
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F49543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:nuc-dot-plot' on page 343 undefined on input line
 1269.


(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B39543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/6655B5CD97C33186A22E6897501301FF9543DFECA235A69AE23006BA05B
4EB70.pygtex [343])
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:nuc-dot-plot-scatter' on page 344 undefined on in
put line 1345.

[344 <./images/dot_plot_scatter.png>]
(./_minted-Tutorial/601CCA4B782F1DA528DB81B0248031959543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `fig:paired-end-qual-plot' on page 345 undefined on in
put line 1406.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `chapter:align' on page 345 undefined on input line 14
18.


LaTeX Warning: Reference `chapter:align' on page 345 undefined on input line 14
25.


(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC739543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:consensus' on page 345 undefined on input line 14
36.


LaTeX Warning: Reference `sec:pssm' on page 345 undefined on input line 1437.

[345]

LaTeX Warning: Reference `sec:getting_info_content' on page 346 undefined on in
put line 1438.


LaTeX Warning: Reference `sec:sub_matrix' on page 346 undefined on input line 1
439.


LaTeX Warning: Reference `sec:summary_info' on page 346 undefined on input line
 1445.


(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA39543DFECA235A69AE23006BA05B
4EB70.pygtex) [346 <./images/SRR001666.png>]
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA48145359543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529
[]\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l
ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c
mr/m/n/10 .

(./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFFBD02851C2FB632864165FCA4920
46548.pygtex [347])

LaTeX Warning: Reference `sec:summary_info' on page 348 undefined on input line
 1565.


(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB5300659543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A409543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D0439543DFECA235A69AE23006BA05B
4EB70.pygtex [348])
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C973BD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `sec:align_clustal' on page 349 undefined on input lin
e 1640.


(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FABD02851C2FB632864165FCA4920
46548.pygtex [349])
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C0717BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C37BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B49407915BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BFBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704
\OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 
val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec
ted_frequencies[^^MD^^M, ^^ME^^M]

(./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF74BD02851C2FB632864165FCA4920
46548.pygtex [350])
(./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4FBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 351 undefined on input line 17
48.

) [351] (./Tutorial/chapter_testing.tex
Chapter 21.

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD062144BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0444BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907344BBF456F55B5DC060035246D76
9EADB.pygtex)

LaTeX Warning: Reference `sec:doctest' on page 352 undefined on input line 55.


(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D44BBF456F55B5DC060035246D76
9EADB.pygtex)
Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77
[]\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte
st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT
1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase
[352]
(./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED44BBF456F55B5DC060035246D76
9EADB.pygtex [353])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A79543DFECA235A69AE23006BA05B
4EB70.pygtex) [354]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706E9543DFECA235A69AE23006BA05B
4EB70.pygtex [355])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F444BBF456F55B5DC060035246D76
9EADB.pygtex)

LaTeX Warning: Reference `sec:doctest' on page 356 undefined on input line 282.



(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA299543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B82977119543DFECA235A69AE23006BA05B
4EB70.pygtex [356])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76
9EADB.pygtex) [357]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345644BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4344BBF456F55B5DC060035246D76
9EADB.pygtex)) [358] (./Tutorial/chapter_contributing.tex
Chapter 22.

LaTeX Warning: Reference `chapter:cookbook' on page 359 undefined on input line
 32.

[359]
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3644BBF456F55B5DC060035246D76
9EADB.pygtex)

LaTeX Warning: Reference `chapter:testing' on page 360 undefined on input line 
75.


LaTeX Warning: Reference `chapter:testing' on page 360 undefined on input line 
91.

[360]) [361] (./Tutorial/chapter_appendix.tex
Chapter 23.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D32BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A4628599543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B429543DFECA235A69AE23006BA05B
4EB70.pygtex [362])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C429543DFECA235A69AE23006BA05B
4EB70.pygtex)

LaTeX Warning: Reference `sec:SeqIO_compressed' on page 363 undefined on input 
line 91.


(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A203BD02851C2FB632864165FCA4920
46548.pygtex)) [363] [364] [365] [366] (./Tutorial.aux
(./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux)
(./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux)
(./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux)
(./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux)
(./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux)
(./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux)
(./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux)
(./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux)
(./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux)
(./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux)
(./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux)
(./Tutorial/chapter_appendix.aux))
kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000
mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied
mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000
This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf)

(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf
(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf)
(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf
(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf
 Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf
 Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf
 Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf
 Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29])
(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf
 Ok [100] [109] [98] [99] [108])
(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf
 Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44]
[45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95]
[96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137]
[138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149]
[150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161]
[162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174]
[175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246])
(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf
 Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57])
(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf
 Ok [185] [178] [179] [170] [186])
(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf
 Ok [188] [189] [190]) ) ) )
(some charht values had to be adjusted by as much as 0.06943pt)
Font metrics written on tcrm1000.tfm.
Output written on tcrm1000.600gf (128 characters, 23548 bytes).
Transcript written on tcrm1000.log.
mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated.


LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.


Package rerunfilecheck Warning: File `Tutorial.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb
xti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmitt10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmr5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on Tutorial.pdf (367 pages, 2963652 bytes).
Transcript written on Tutorial.log.
pdflatex --shell-escape "\def\bpversion{1.81}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2023-06-01> patch level 1
L3 programming layer <2023-08-29>
(./Tutorial.tex (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty)
(/usr/share/texmf/tex/latex/misc/hevea.sty
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') Excluding comment 'rawhtml'
Excluding comment 'htmlonly')
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/lineno/lineno.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/shellesc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/ifplatform/ifplatform.sty
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))
(/usr/share/texlive/texmf-dist/tex/generic/catchfile/catchfile.sty
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty))
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty) (./Tutorial.w18)
) (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.sty
(/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.tex))
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 70.

(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))/usr/bin/pygmentize

(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./Tutorial.aux (./Tutorial/chapter_introduction.aux)
(./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux)
(./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux)
(./Tutorial/chapter_align.aux

LaTeX Warning: Label `sec:pairwise-general-gapscores' multiply defined.

) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux)
(./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux)
(./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux)
(./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux)
(./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux)
(./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux)
(./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux)
(./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux)
(./Tutorial/chapter_appendix.aux))
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(./Tutorial.out) (./Tutorial.out) Excluding 'htmlonly' comment.
Excluding 'rawhtml' comment. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.m
ap} <./images/biopython_logo.pdf>] (./Tutorial.toc
pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has 
been already used, duplicate ignored
<to be read again> 
                   \relax 
l.39 ...tions and locations}{30}{subsection.4.3.2}
                                                  % [1] [2] [3] [4] [5]
[6] [7]) [8] (./Tutorial/chapter_introduction.tex
Chapter 1.
[9] [10] Excluding 'rawhtml' comment.
Underfull \hbox (badness 10000) in paragraph at lines 122--128


Underfull \hbox (badness 10000) in paragraph at lines 134--136

(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/C3217FD04973F24516F5530BB525A22CBD02851C2FB632864165FCA4920
46548.pygtex) [11 <./images/biopython_logo_old.jpg>]
Overfull \hbox (2.99303pt too wide) in paragraph at lines 187--189
\OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor
t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or
 see [][]$\OT1/cmtt/m/n/10 http : / / biopython .
[12]) [13] (./Tutorial/chapter_quick_start.tex
Chapter 2.

LaTeX Warning: Reference `chapter:advanced' on page 14 undefined on input line 
14.


(./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612CBD02851C2FB632864165FCA4920
46548.pygtex [14])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535ABBD02851C2FB632864165FCA4920
46548.pygtex) [15]
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B0213346781855BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26DBD02851C2FB632864165FCA4920
46548.pygtex [16])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F2BD02851C2FB632864165FCA4920
46548.pygtex) [17]) [18] (./Tutorial/chapter_seq_objects.tex
Chapter 3.

(./_minted-Tutorial/048D805D0CE39D0271B0A9A9F6FA0B90BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDCBD02851C2FB632864165FCA4920
46548.pygtex) [19]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0F44B540F3531194878FC29AF017902BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E97622504BD02851C2FB632864165FCA4920
46548.pygtex [20])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E36BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D9386420BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/732D927996C79742AC990312B3D6EEB0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C270BD02851C2FB632864165FCA4920
46548.pygtex [21])
(./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC47BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D394BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8DBD02851C2FB632864165FCA4920
46548.pygtex [22])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF17BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC0BD02851C2FB632864165FCA4920
46548.pygtex [23])
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C8753BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B386BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A70BD02851C2FB632864165FCA4920
46548.pygtex [24])
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF82BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD64BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF98BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE79BD02851C2FB632864165FCA4920
46548.pygtex [25])
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B55990BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874DBD02851C2FB632864165FCA4920
46548.pygtex [26])
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/06DBC59F2EAD33E7A951888537876615BD02851C2FB632864165FCA4920
46548.pygtex) [27]
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C338BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CB669566ECC2CFEDC7429F829576A
D0DC6.pygtex [28])
(./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E84BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DFDB859800920408E228736AD921B5DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B040BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE451BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2EBD02851C2FB632864165FCA4920
46548.pygtex [29])
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C0BD02851C2FB632864165FCA4920
46548.pygtex)) [30] [31] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

(./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC809BD02851C2FB632864165FCA4920
46548.pygtex) [32]
(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D407BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC2BD02851C2FB632864165FCA4920
46548.pygtex [33])
(./_minted-Tutorial/510764EE0BB38AD6C688E71989677507669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D849822BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD2085BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9669566ECC2CFEDC7429F829576A
D0DC6.pygtex [34])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA601BD02851C2FB632864165FCA4920
46548.pygtex [35])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F926BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0DBD02851C2FB632864165FCA4920
46548.pygtex) [36] [37]
(./_minted-Tutorial/AD47AD29D6F7927F9406BE5609676388BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F3BD02851C2FB632864165FCA4920
46548.pygtex [38])
(./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D86C559003980DC8749AF92530435DFDBD02851C2FB632864165FCA4920
46548.pygtex) [39]
(./_minted-Tutorial/1C0A562378DEEE8E210765437B3E1700BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B49BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C75BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0C3ED75879971F09D72A92585654A32CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E3920BD02851C2FB632864165FCA4920
46548.pygtex [40])
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F9689BD02851C2FB632864165FCA4920
46548.pygtex [41])
(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B2340BD02851C2FB632864165FCA4920
46548.pygtex [42])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEBBD02851C2FB632864165FCA4920
46548.pygtex [43])
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A85BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B311BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D2457BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF82BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDFBD02851C2FB632864165FCA4920
46548.pygtex [44])
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF1718501669BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1BBD02851C2FB632864165FCA4920
46548.pygtex [45])
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED36BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E7BD02851C2FB632864165FCA4920
46548.pygtex) [46]
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B63BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B8793BD02851C2FB632864165FCA4920
46548.pygtex)) [47] (./Tutorial/chapter_seqio.tex
Chapter 5.

(./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D498BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB6789543DFECA235A69AE23006BA05B
4EB70.pygtex [48])
(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE5009549543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F19543DFECA235A69AE23006BA05B
4EB70.pygtex [49])
(./_minted-Tutorial/C82398A4A04383A063D2E648811230529543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [50]
(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD1622219543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD829543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE6BD02851C2FB632864165FCA4920
46548.pygtex [51])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E734519543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9562C263804C6DD613F075A435553A9FBD02851C2FB632864165FCA4920
46548.pygtex [52])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C91BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/23394A4616015FFE4619934E98424178BD02851C2FB632864165FCA4920
46548.pygtex [53])
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C09BD02851C2FB632864165FCA4920
46548.pygtex) [54]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD4769543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD89543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D79543DFECA235A69AE23006BA05B
4EB70.pygtex [55])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A49543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989FBD02851C2FB632864165FCA4920
46548.pygtex [56])
(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB03BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF6BD02851C2FB632864165FCA4920
46548.pygtex [57])
(./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/55430EAFE498E385842834603E0B8C869543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB89543DFECA235A69AE23006BA05B
4EB70.pygtex [58])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C178893BD02851C2FB632864165FCA4920
46548.pygtex) [59]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C78BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF4065BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A364BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920
46548.pygtex [60])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853
\OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org /
 pub / databases / uniprot / current _ release / knowledgebase / complete /

(./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894
[]\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u
p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1
/cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76
9EADB.pygtex [61])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A2777BD02851C2FB632864165FCA4920
46548.pygtex) [62]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C6471BD02851C2FB632864165FCA4920
46548.pygtex) [63]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD73429543DFECA235A69AE23006BA05B
4EB70.pygtex [64])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4669566ECC2CFEDC7429F829576A
D0DC6.pygtex [65])
(./_minted-Tutorial/C194E2231D844AE7D0223173D2A899919543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEABD02851C2FB632864165FCA4920
46548.pygtex) [66]
(./_minted-Tutorial/920133226A22EEB682D854077D7FB78FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C260028BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920
46548.pygtex) [67]
(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351
\OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) 
[]\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm
tt/m/n/10 SeqRecord.format(...)
[68]
(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397
[]\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm
tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt
/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B
4EB70.pygtex)) [69] (./Tutorial/chapter_align.tex
Chapter 6.

(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42669566ECC2CFEDC7429F829576A
D0DC6.pygtex [70])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AECBD02851C2FB632864165FCA4920
46548.pygtex [71])
(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A31077BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [72]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C560407BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533669566ECC2CFEDC7429F829576A
D0DC6.pygtex [73])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF756BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [74]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020669566ECC2CFEDC7429F829576A
D0DC6.pygtex [75])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [76]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D318BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477669566ECC2CFEDC7429F829576A
D0DC6.pygtex [77])
Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435
\OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t
or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()

Overfull \hbox (39.68698pt too wide) in paragraph at lines 442--447
[][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u
s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just
 use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert()

(./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F4024BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F669566ECC2CFEDC7429F829576A
D0DC6.pygtex [78])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99669566ECC2CFEDC7429F829576A
D0DC6.pygtex [79])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F169543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56669566ECC2CFEDC7429F829576A
D0DC6.pygtex [80])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2590B11C695B984E246A0A91734F786CBD02851C2FB632864165FCA4920
46548.pygtex) [81]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE5BD02851C2FB632864165FCA4920
46548.pygtex [82])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B71692BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB00BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E59BD02851C2FB632864165FCA4920
46548.pygtex [83])
(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A9253BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AE857C14E4731CC6F6EBA53051460097BD02851C2FB632864165FCA4920
46548.pygtex) [84]
(./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/523928538FA511A925EC995B1803BD16BD02851C2FB632864165FCA4920
46548.pygtex) [85]
(./_minted-Tutorial/CD47D1913C82182C164BD47DA4715282BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E893BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C63064BD02851C2FB632864165FCA4920
46548.pygtex) [86]
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A442BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F986368BD02851C2FB632864165FCA4920
46548.pygtex [87])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130
[]\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi
le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO

(./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BDBD02851C2FB632864165FCA4920
46548.pygtex [88])
(./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F739998BD02851C2FB632864165FCA4920
46548.pygtex [89])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E7454BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5CBD02851C2FB632864165FCA4920
46548.pygtex [90])
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE74BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A240BD02851C2FB632864165FCA4920
46548.pygtex) [91]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/39152F199CEBB3375366F2E947824519BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF385674BD02851C2FB632864165FCA4920
46548.pygtex [92])
(./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE2493BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DF151703751D72BD556402B910190A87BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA88BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/554024580088332FAF0EA9296BACE82EBD02851C2FB632864165FCA4920
46548.pygtex) [93]
(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E361BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6CCC707502EDD92E9C355854215BF885BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C5BD02851C2FB632864165FCA4920
46548.pygtex [94])
(./_minted-Tutorial/E5E00F47BD7A0C8BC5F8818526283868BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE04BD02851C2FB632864165FCA4920
46548.pygtex) [95]
(./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/48453D528762FF183499778647AF218BBD02851C2FB632864165FCA4920
46548.pygtex [96])
(./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A39BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix
 []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu
tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt
t/m/n/10 aligner.mismatch_score

Overfull \hbox (47.73264pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat
rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t
ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt
/m/n/10 aligner.mismatch_score

LaTeX Warning: `h' float specifier changed to `ht'.


Overfull \hbox (32.852pt too wide) in paragraph at lines 1776--1820
[][]

(./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CEBD02851C2FB632864165FCA4920
46548.pygtex [97]) [98] [99]
(./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514ABD02851C2FB632864165FCA4920
46548.pygtex) [100]
(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE1911BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB8671BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EFBD02851C2FB632864165FCA4920
46548.pygtex [101])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D01BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9FBD02851C2FB632864165FCA4920
46548.pygtex [102])
(./_minted-Tutorial/0758643069FF669538B9540ECD26C94CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A34296592BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/76E331C5187C259B69198E91FC4AD112BD02851C2FB632864165FCA4920
46548.pygtex [103])
(./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD357BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966BBD02851C2FB632864165FCA4920
46548.pygtex [104])
(./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/66AABFA387595237A8CE2518915213F8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B15E737F9393063B641148640673D991BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B46BD02851C2FB632864165FCA4920
46548.pygtex [105])
(./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/874975627BAB24A36A35FD4C633D246DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BDBD02851C2FB632864165FCA4920
46548.pygtex [106])
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A7BD02851C2FB632864165FCA4920
46548.pygtex [107])
(./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/52868B2F44504455E4969FEF2614B63BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB94BD02851C2FB632864165FCA4920
46548.pygtex) [108]
(./_minted-Tutorial/E7E68A8851DEEE300947A0531513417DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF65BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA1733BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6502BA65433924876427DBB6013C1003BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FDBD02851C2FB632864165FCA4920
46548.pygtex [109])
(./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F1012BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA5077BD02851C2FB632864165FCA4920
46548.pygtex [110])
(./_minted-Tutorial/779C61444C54C1736794F4E11B0E326DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E105BD02851C2FB632864165FCA4920
46548.pygtex [111])
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA77BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF796600BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613
\OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments 
is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing
 [][]\OT1/cmtt/m/n/10 len(alignments)

(./_minted-Tutorial/F89522EF58FB067C6521C367C7134716BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE20BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9CBD02851C2FB632864165FCA4920
46548.pygtex [112])
(./_minted-Tutorial/882BD2544386DECA236BF25C7DD64857BD02851C2FB632864165FCA4920
46548.pygtex [113])
(./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA70BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A29BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/13D646E6B49807044DBDC43707A09846BD02851C2FB632864165FCA4920
46548.pygtex [114])
(./_minted-Tutorial/467CA50C36874E405E988587FEC07686BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E62BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A94C18D2207C354646F831D57FD85B35BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D8BD02851C2FB632864165FCA4920
46548.pygtex [115])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A73BD02851C2FB632864165FCA4920
46548.pygtex [116])
(./_minted-Tutorial/AAF53200644F4F68779FB844730087D3BD02851C2FB632864165FCA4920
46548.pygtex [117])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE06BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057DBD02851C2FB632864165FCA4920
46548.pygtex [118])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/842D73F66680850822D006857AE71FE7BD02851C2FB632864165FCA4920
46548.pygtex) [119]
(./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE3135BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7C466424D72F09AE5AACA884161416F9BD02851C2FB632864165FCA4920
46548.pygtex [120])
(./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA825278BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F680093BD02851C2FB632864165FCA4920
46548.pygtex [121])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315ECBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D86241664707BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5669566ECC2CFEDC7429F829576A
D0DC6.pygtex [122])
(./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/60D893638743BD147116D13E00593D6CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D669566ECC2CFEDC7429F829576A
D0DC6.pygtex [123])
(./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9EDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6DBD02851C2FB632864165FCA4920
46548.pygtex [124])
(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F2519BD02851C2FB632864165FCA4920
46548.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED0BD02851C2FB632864165FCA4920
46548.pygtex) [125]
(./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F120EF3444F3192D48657B4E52407017BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F2091BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5DBD02851C2FB632864165FCA4920
46548.pygtex [126])
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C71BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75ABD02851C2FB632864165FCA4920
46548.pygtex [127])) [128] (./Tutorial/chapter_blast.tex
Chapter 7.

Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46
[]\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas
t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs 
&
[129]
(./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4EBD02851C2FB632864165FCA4920
46548.pygtex [130])
(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920
46548.pygtex) [131]
(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE4792BD02851C2FB632864165FCA4920
46548.pygtex) [132]
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE5218004BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F40394BD02851C2FB632864165FCA4920
46548.pygtex [133])
(./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D238BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68259DF5B1930070C029D5A72D891A36BD02851C2FB632864165FCA4920
46548.pygtex [134])
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924669566ECC2CFEDC7429F829576A
D0DC6.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.

LaTeX Warning: Float too large for page by 32.27644pt on input line 481.

) [135] [136 <./images/BlastRecord.png>] [137 <./images/PSIBlastRecord.png>]
(./Tutorial/chapter_searchio.tex
Chapter 8.

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [138]
Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93
[][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle 
con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10
 HSPFragment

Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107
[][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files
 with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/
m/n/10 QueryResult

(./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FCBD02851C2FB632864165FCA4920
46548.pygtex [139])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B51955BD02851C2FB632864165FCA4920
46548.pygtex [140])
(./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/362861C831165FEA5413E0240053CD89BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE327BD02851C2FB632864165FCA4920
46548.pygtex [141])
(./_minted-Tutorial/FD9C81C098491598DBFB6208173BB575BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A03BD02851C2FB632864165FCA4920
46548.pygtex) [142]
(./_minted-Tutorial/0B914838010D3E86EC368E1702EB7253BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E619BD02851C2FB632864165FCA4920
46548.pygtex [143])
(./_minted-Tutorial/DDECA9EB99D9FA38003A52C176593072BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/578CBF904F35965EECFEC1FA694F0752BD02851C2FB632864165FCA4920
46548.pygtex [144])
(./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD64BD02851C2FB632864165FCA4920
46548.pygtex) [145]
(./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC6246863BD02851C2FB632864165FCA4920
46548.pygtex) [146]
(./_minted-Tutorial/A3385B945E43CC076FFA693B27681F05BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE573577BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B46BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD95BD02851C2FB632864165FCA4920
46548.pygtex [147])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD880444BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C787BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745
[]\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10
 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr
/m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment

(./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920
46548.pygtex [148])
(./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920
46548.pygtex [149])
(./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920
46548.pygtex [150])
(./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920
46548.pygtex) [151]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059
\OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT
1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like 
[][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F4BD02851C2FB632864165FCA4920
46548.pygtex) [152]
Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092
[]\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us
-ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt
/m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E9868BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE55BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DEBD02851C2FB632864165FCA4920
46548.pygtex) [153]
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170
[]\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 
also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic
h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse

(./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C176BD02851C2FB632864165FCA4920
46548.pygtex)) [154] (./Tutorial/chapter_entrez.tex
Chapter 9.
[155]
(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB5BD02851C2FB632864165FCA4920
46548.pygtex) [156]
(./_minted-Tutorial/7692669934D8ED6DEE1B8B6684745421BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA36BD02851C2FB632864165FCA4920
46548.pygtex [157])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C008BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FACBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F6BD02851C2FB632864165FCA4920
46548.pygtex [158])
(./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C68BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D50277BD02851C2FB632864165FCA4920
46548.pygtex) [159]
(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19FBD02851C2FB632864165FCA4920
46548.pygtex) [160]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F3147BD02851C2FB632864165FCA4920
46548.pygtex [161] [162])
(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D59543DFECA235A69AE23006BA05B
4EB70.pygtex [163])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F487BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF008BD02851C2FB632864165FCA4920
46548.pygtex [164])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68622353B578A611D2F621023E3C4BD1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F70BD02851C2FB632864165FCA4920
46548.pygtex [165])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC38BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0944BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722ABD02851C2FB632864165FCA4920
46548.pygtex [166])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF38669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0BBD02851C2FB632864165FCA4920
46548.pygtex [167])
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B669566ECC2CFEDC7429F829576A
D0DC6.pygtex [168])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6EF35C66998219AA15568E5FA366261EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD3676C48A9629929A55320028B512E5BD02851C2FB632864165FCA4920
46548.pygtex [169])
(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD669566ECC2CFEDC7429F829576A
D0DC6.pygtex [170])
(./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC12BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D75BD02851C2FB632864165FCA4920
46548.pygtex [171])
(./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E277BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A1266BD02851C2FB632864165FCA4920
46548.pygtex [172])
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019669566ECC2CFEDC7429F829576A
D0DC6.pygtex [173])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B624BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA5BD02851C2FB632864165FCA4920
46548.pygtex) [174]
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA19543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1EBD02851C2FB632864165FCA4920
46548.pygtex [175])
(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/964257041BEB9E732FF9A943209BD6EDBD02851C2FB632864165FCA4920
46548.pygtex [176])
(./_minted-Tutorial/600193D5D5D44162E61A3CAB40448426BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B642038BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A1BD02851C2FB632864165FCA4920
46548.pygtex [177])
(./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FDBD02851C2FB632864165FCA4920
46548.pygtex [178])
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A72797BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB3848BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D76169664531538D144C55FFC33571BBD02851C2FB632864165FCA4920
46548.pygtex) [179]
(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C45BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB93649BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D8BD02851C2FB632864165FCA4920
46548.pygtex) [180]
(./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C477BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E24BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F9633BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D5749543DFECA235A69AE23006BA05B
4EB70.pygtex [181])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA9543DFECA235A69AE23006BA05B
4EB70.pygtex) [182]
(./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927ABD02851C2FB632864165FCA4920
46548.pygtex)) [183] (./Tutorial/chapter_uniprot.tex
Chapter 10.

(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A86BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A668BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD6768BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/930B60BD569CAAF368B0E614553F3030BD02851C2FB632864165FCA4920
46548.pygtex) [184]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA6519182BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB934669BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD69228BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D14BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C06BD02851C2FB632864165FCA4920
46548.pygtex [185])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A4517918BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09ABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224669566ECC2CFEDC7429F829576A
D0DC6.pygtex [186])
(./_minted-Tutorial/956383F4066B9E093C9D2E3843CA0220BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307BBD02851C2FB632864165FCA4920
46548.pygtex [187])
(./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E2BD02851C2FB632864165FCA4920
46548.pygtex) [188]
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC783BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF9BD02851C2FB632864165FCA4920
46548.pygtex [189])
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B622BD02851C2FB632864165FCA4920
46548.pygtex [190])
Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366
[]\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n
/10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/
m/n/10 SwissProt.read(handle)

(./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87DBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410
[]\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m
en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re
cord

(./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B753BD02851C2FB632864165FCA4920
46548.pygtex) [191]
(./_minted-Tutorial/9457A436D281E066D350873A88476E59BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E7BD02851C2FB632864165FCA4920
46548.pygtex [192])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E86169BD02851C2FB632864165FCA4920
46548.pygtex)) [193] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C22853BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E69085BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C71BD02851C2FB632864165FCA4920
46548.pygtex [194])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA7388BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB35BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB8231BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879EBD02851C2FB632864165FCA4920
46548.pygtex) [195]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E18BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D176BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A024BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A5BD02851C2FB632864165FCA4920
46548.pygtex) [196]
(./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB136BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECECBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA4BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264
\OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m
/n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato
m)
[197] Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D979BD02851C2FB632864165FCA4920
46548.pygtex) [198] [199 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD855BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB247BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E2727622BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A12BD02851C2FB632864165FCA4920
46548.pygtex) [200]
(./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DCBD02851C2FB632864165FCA4920
46548.pygtex) [201]
(./_minted-Tutorial/35E34E333445AAAA4E33570211335BA5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B1BD02851C2FB632864165FCA4920
46548.pygtex [202])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC88098BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB12492BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/76657140082404C594EE786B642215C3BD02851C2FB632864165FCA4920
46548.pygtex [203])
(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254CBD02851C2FB632864165FCA4920
46548.pygtex) [204]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB90BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B128BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B3BD02851C2FB632864165FCA4920
46548.pygtex [205])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF231899BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A624BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC2663BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA39BD02851C2FB632864165FCA4920
46548.pygtex [206])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E667BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899BBD02851C2FB632864165FCA4920
46548.pygtex [207])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AE729029ED6ABA2E38F17FAA1C60732CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8BB12A44CF293B1BF656E236EFE0BE12BD02851C2FB632864165FCA4920
46548.pygtex [208])
(./_minted-Tutorial/F0EFB999D116D041397B95C62B2EED29BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FE5531F727D4D28736FC18DF8A430EBBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E045C9432637E8C515E37CB4917FD57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AD9DB5C434FCB2537E43EF340112BD08BD02851C2FB632864165FCA4920
46548.pygtex [209])
(./_minted-Tutorial/C1D5880B46A9CAEDCEB7F545F21B98CBBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (4.2397pt too wide) in paragraph at lines 1070--1074
\OT1/cmr/m/n/10 Missing atoms and other is-sues can cause prob-lems when re-bui
ld-ing a struc-ture. Use \OT1/cmtt/m/n/10 structure[]rebuild[]test$$

(./_minted-Tutorial/BD4323A41DFED2A7E4CD261AA65F95EDBD02851C2FB632864165FCA4920
46548.pygtex) [210]
(./_minted-Tutorial/6395F38A139598C6CC297CDBA73A8A43BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/21D2C13C2AA9395E0B1E4F1DDC801798BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/12E711A2CBFD0B046AA026208A117C1E9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/813FE78A3F8D8E46F06FF71539F000E69543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/CD78F368EB103F71947A3184BB62B46F9543DFECA235A69AE23006BA05B
4EB70.pygtex [211])
(./_minted-Tutorial/8E34478E945971E05C77F0A0E8C1B9D89543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/0D3FBB23D21A6A468370D56058193010BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BBA5405CCC4A3178ADA49DA358246C819543DFECA235A69AE23006BA05B
4EB70.pygtex [212])
(./_minted-Tutorial/DE601B1883F045FBEE1B28168CFF0CCABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AAF43F15691D49893FAEEAB7B7693A1D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/0ABBC5325B76EBCC5687BB33E7595F219543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment. [213 <./images/1a8o-ca-plot.png>]
Overfull \hbox (15.27203pt too wide) in paragraph at lines 1292--1295
[]\OT1/cmr/m/n/10 This work uses equa-tions de-vel-oped by Blue, the Hedronome-
ter, dis-cussed in [][]$\OT1/cmtt/m/n/10 https : / / math . stackexchange .

Overfull \hbox (116.15723pt too wide) in paragraph at lines 1292--1295
\OT1/cmtt/m/n/10 com / a / 49340 / 409$[][] \OT1/cmr/m/n/10 and fur-ther in [][
]$\OT1/cmtt/m/n/10 http : / / daylateanddollarshort . com / mathdocs / Heron-[]
like-[]Results-[]for-[]Tetrahedral-[]Volume .

(./_minted-Tutorial/BACD9263B6DB9FE9B9C8FA59C017D190BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2AECB4AED1E5DFDC387B42EF509CC3F4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1D3E5D8C6C6880A4C1D7DC0DEE7DC0C7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/815743EBD76EB14B6A71E1A4AE6433A4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B285099D410967E19F3165C7B5395544BD02851C2FB632864165FCA4920
46548.pygtex [214]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/5DFAFA7DE84292336F50FFB5DD8AD22A9543DFECA235A69AE23006BA05B
4EB70.pygtex [215 <./images/phe-pairs-3pbl.png>])
(./_minted-Tutorial/ED5201F27B6F2CC7A881AC419DF87B5E9543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (214.06847pt too wide) in paragraph at lines 1458--1474
[][] 
[216]
(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993CBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Command \r invalid in math mode on input line 1527.


(./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705EBD02851C2FB632864165FCA4920
46548.pygtex [217])
(./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C6709BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/895E3343902EFB0E5475667B01C4B691BD02851C2FB632864165FCA4920
46548.pygtex [218]) [219]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB15BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A9BD02851C2FB632864165FCA4920
46548.pygtex [220])
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A74BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5DBD02851C2FB632864165FCA4920
46548.pygtex) [221]) [222] (./Tutorial/chapter_popgen.tex
Chapter 12.

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6B9543DFECA235A69AE23006BA05B
4EB70.pygtex) [223]
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC9543DFECA235A69AE23006BA05B
4EB70.pygtex)) [224] (./Tutorial/chapter_phylo.tex
Chapter 13.

(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15844BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C24BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4ADBD02851C2FB632864165FCA4920
46548.pygtex [225])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920
46548.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBABD02851C2FB632864165FCA4920
46548.pygtex) [226]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1ADBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185
[]\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t
he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor

(./_minted-Tutorial/29624A9666C9430AABADF395148BBF27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920
46548.pygtex [227 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9BBD02851C2FB632864165FCA4920
46548.pygtex [228 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/456F5679DCD4FF740E7A110889D86573BD02851C2FB632864165FCA4920
46548.pygtex [229])
(./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F55BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D3BD02851C2FB632864165FCA4920
46548.pygtex [230])
(./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEEBD02851C2FB632864165FCA4920
46548.pygtex) Excluding 'htmlonly' comment. [231 <./images/phylo-draw-example.p
ng>]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486
\OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, 
[][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"})
[232]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537
[]\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, 
find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10
 ,
[233]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B
4EB70.pygtex) [234]
Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707
[]\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter
-act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier .

(./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD8119BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095BBD02851C2FB632864165FCA4920
46548.pygtex) [235]
(./_minted-Tutorial/0702C9875263768417DD3ED2EF78755EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D2BD02851C2FB632864165FCA4920
46548.pygtex) [236]) [237] (./Tutorial/chapter_motifs.tex
Chapter 14.

(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486ABD02851C2FB632864165FCA4920
46548.pygtex [238])
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D03BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE75BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D177BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D257173BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/86717C2BCE65F41FCDB8652763165857BD02851C2FB632864165FCA4920
46548.pygtex [239])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F61243192022BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB2476BD02851C2FB632864165FCA4920
46548.pygtex) [240]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA669566ECC2CFEDC7429F829576A
D0DC6.pygtex [241])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECDBD02851C2FB632864165FCA4920
46548.pygtex [242])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C76BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92669566ECC2CFEDC7429F829576A
D0DC6.pygtex [243])
(./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F706BD02851C2FB632864165FCA4920
46548.pygtex [244])
(./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DCBD02851C2FB632864165FCA4920
46548.pygtex [245])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFDBD02851C2FB632864165FCA4920
46548.pygtex [246])
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C378BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6BBD02851C2FB632864165FCA4920
46548.pygtex [247])
(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44669566ECC2CFEDC7429F829576A
D0DC6.pygtex [248])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909FBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606
\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man
d reads the com-plete file di-rectly, so you can close the file af-ter call-ing
 [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B84BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB6BD02851C2FB632864165FCA4920
46548.pygtex [249])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E012053BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7669566ECC2CFEDC7429F829576A
D0DC6.pygtex [250])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5CBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: `h' float specifier changed to `ht'.

[251]
(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EFBD02851C2FB632864165FCA4920
46548.pygtex [252])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F26406BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF51495BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE70605BD02851C2FB632864165FCA4920
46548.pygtex [253])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C74BD02851C2FB632864165FCA4920
46548.pygtex [254])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C98812BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E225BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E48BD02851C2FB632864165FCA4920
46548.pygtex [255])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7BBD02851C2FB632864165FCA4920
46548.pygtex [256])
(./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A81BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA161BD02851C2FB632864165FCA4920
46548.pygtex) [257]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E25BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A5092BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C86073BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE970BD02851C2FB632864165FCA4920
46548.pygtex [258])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF4BD02851C2FB632864165FCA4920
46548.pygtex [259])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E322BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD7261603BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA2473BD02851C2FB632864165FCA4920
46548.pygtex [260])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA16BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D3BD02851C2FB632864165FCA4920
46548.pygtex) [261]
(./_minted-Tutorial/868ABF9ABD2736A12F423306646D7706BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/912C817861E626118AB2FA06F12910B6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A26BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [262]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB41BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B6BD02851C2FB632864165FCA4920
46548.pygtex) [263]) [264] (./Tutorial/chapter_cluster.tex
Chapter 15.
[265] [266] [267] [268]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C2B72A7408C7DF74DFCEBE0485997287BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE601735827BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A25009543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C0BD02851C2FB632864165FCA4920
46548.pygtex [269])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246
\OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra
nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$

(./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB34BD02851C2FB632864165FCA4920
46548.pygtex) [270] [271]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762EBD02851C2FB632864165FCA4920
46548.pygtex) [272]
(./_minted-Tutorial/C286E2777B917B774560CBDC7CF92626BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B
4EB70.pygtex) [273] [274]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424
[][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them.
 The items be-ing clus-tered are num-bered from 0 to $[]$,

(./_minted-Tutorial/015798D317E9D8732518AFD186C997CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C239049267861739BD02851C2FB632864165FCA4920
46548.pygtex) [275]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE22BD02851C2FB632864165FCA4920
46548.pygtex) [276]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F72BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D41BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF8895055BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEBBD02851C2FB632864165FCA4920
46548.pygtex [277])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B
4EB70.pygtex) [278]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C175BD02851C2FB632864165FCA4920
46548.pygtex) [279]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEABD02851C2FB632864165FCA4920
46548.pygtex) [280]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961CBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750
 [] 
[281] [282]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FCBD02851C2FB632864165FCA4920
46548.pygtex) [283]
(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E0BD02851C2FB632864165FCA4920
46548.pygtex [284])
(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA8504BD02851C2FB632864165FCA4920
46548.pygtex) [285]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D70BD02851C2FB632864165FCA4920
46548.pygtex [286])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF58BD02851C2FB632864165FCA4920
46548.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116
[]\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result
_K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT
1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 
. 
[287] (./Tutorial/chapter_learning.tex
Chapter 16.
[288]
(./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4DBD02851C2FB632864165FCA4920
46548.pygtex [289])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4FBD02851C2FB632864165FCA4920
46548.pygtex [290])
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB096BD02851C2FB632864165FCA4920
46548.pygtex [291])
(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D402BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A012BD02851C2FB632864165FCA4920
46548.pygtex [292])

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 267.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 267.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 275.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 275.


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E6BD02851C2FB632864165FCA4920
46548.pygtex) [293]

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 287.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 287.


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA595BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B38BF6A3D910590D450B331A075B723CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC1BD02851C2FB632864165FCA4920
46548.pygtex [294])
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC15BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A586FFDD9483C890754DBE5DFC420710BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D35BD02851C2FB632864165FCA4920
46548.pygtex [295])) [296] (./Tutorial/chapter_graphics.tex
Chapter 17.
[297]
(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A09543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D8169543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B0359543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA79543DFECA235A69AE23006BA05B
4EB70.pygtex [298]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E9543DFECA235A69AE23006BA05B
4EB70.pygtex [299 <./images/plasmid_linear.png (PNG copy)>]) [300 <./images/pla
smid_circular.png (PNG copy)>]
(./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF279543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A7359543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D8509543DFECA235A69AE23006BA05B
4EB70.pygtex [301]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B949543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C9543DFECA235A69AE23006BA05B
4EB70.pygtex [302] [303 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/67B3F646AA5F8690151428081229D39B9543DFECA235A69AE23006BA05B
4EB70.pygtex [304] [305 <./images/GD_sigils.png>] [306 <./images/GD_sigil_arrow
_shafts.png>] [307 <./images/GD_sigil_arrow_heads.png>] [308])
Excluding 'htmlonly' comment. [309 <./images/plasmid_linear_nice.png (PNG copy)
>] [310 <./images/plasmid_circular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA899543DFECA235A69AE23006BA05B
4EB70.pygtex [311])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177A9543DFECA235A69AE23006BA05B
4EB70.pygtex [312]) Excluding 'htmlonly' comment. [313 <./images/three_track_si
mple.png>]
(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA1119543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB9543DFECA235A69AE23006BA05B
4EB70.pygtex [314])
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD18409543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C289543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879
[]\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the
 [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm
tt/m/n/10 cross_track_links
Excluding 'htmlonly' comment. [315] Excluding 'htmlonly' comment. [316 <./image
s/three_track_cl.png>] [317 <./images/three_track_cl2a.png>]
(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F7284149779543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F9543DFECA235A69AE23006BA05B
4EB70.pygtex) [318]
(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C9543DFECA235A69AE23006BA05B
4EB70.pygtex [319] [320 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A759543DFECA235A69AE23006BA05B
4EB70.pygtex [321]) Excluding 'htmlonly' comment.) [322]
(./Tutorial/chapter_kegg.tex
Chapter 18.

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C71BD02851C2FB632864165FCA4920
46548.pygtex) [323]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B9543DFECA235A69AE23006BA05B
4EB70.pygtex [324])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95669566ECC2CFEDC7429F829576A
D0DC6.pygtex)) [325] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8DBD02851C2FB632864165FCA4920
46548.pygtex) [326]
(./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA9721BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB44BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB081BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF8BD02851C2FB632864165FCA4920
46548.pygtex [327])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D7206BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579DBD02851C2FB632864165FCA4920
46548.pygtex [328])
(./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E0872188BD02851C2FB632864165FCA4920
46548.pygtex [329])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E6BD02851C2FB632864165FCA4920
46548.pygtex)) [330] (./Tutorial/chapter_cookbook.tex
Chapter 20.

(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB9543DFECA235A69AE23006BA05B
4EB70.pygtex [331])
(./_minted-Tutorial/CA0835D76EF6887731674D8AB555091B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E57164BD02851C2FB632864165FCA4920
46548.pygtex) [332]
(./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54F9543DFECA235A69AE23006BA05B
4EB70.pygtex [333])
(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F649543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A02396470619543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B9543DFECA235A69AE23006BA05B
4EB70.pygtex [334])
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC655419543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE4087939543DFECA235A69AE23006BA05B
4EB70.pygtex) [335]
(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA29543DFECA235A69AE23006BA05B
4EB70.pygtex) [336]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF6418319543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F354509543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (5.83499pt too wide) in paragraph at lines 454--458
\OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul
d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B
4EB70.pygtex [337])
Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477
\OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849.
fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[
]primer.fastq\OT1/cmr/m/n/10 . 

(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA5569543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A9543DFECA235A69AE23006BA05B
4EB70.pygtex [338])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C9543DFECA235A69AE23006BA05B
4EB70.pygtex) [339]
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F89159543DFECA235A69AE23006BA05B
4EB70.pygtex) [340]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C319543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC407373679543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D2587BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B69543DFECA235A69AE23006BA05B
4EB70.pygtex [341])
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A09543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582EBD02851C2FB632864165FCA4920
46548.pygtex [342])
(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7DBD02851C2FB632864165FCA4920
46548.pygtex [343])
(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF098BD02851C2FB632864165FCA4920
46548.pygtex) [344]
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052669566ECC2CFEDC7429F829576A
D0DC6.pygtex [345])
(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B79543DFECA235A69AE23006BA05B
4EB70.pygtex [346]) Excluding 'htmlonly' comment.
Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120
[]\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10
 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use
 [][]\OT1/cmtt/m/n/10 pylab.savefig(...)

(./_minted-Tutorial/798776F436EA559BACD9C305C09973919543DFECA235A69AE23006BA05B
4EB70.pygtex [347 <./images/hist_plot.png>])
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
[348 <./images/gc_plot.png>]
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF79543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/80A47C8780CE3021D53829563E8166569543DFECA235A69AE23006BA05B
4EB70.pygtex [349 <./images/dot_plot.png>])
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F49543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B39543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/6655B5CD97C33186A22E6897501301FF9543DFECA235A69AE23006BA05B
4EB70.pygtex [350])
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment. [351 <./images/dot_plot_scatter.png
>]
(./_minted-Tutorial/601CCA4B782F1DA528DB81B0248031959543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC739543DFECA235A69AE23006BA05B
4EB70.pygtex) [352]
(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA39543DFECA235A69AE23006BA05B
4EB70.pygtex) [353 <./images/SRR001666.png>]
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA48145359543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529
[]\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l
ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c
mr/m/n/10 .

(./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFFBD02851C2FB632864165FCA4920
46548.pygtex [354])
(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB5300659543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A409543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D0439543DFECA235A69AE23006BA05B
4EB70.pygtex [355])
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C973BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FABD02851C2FB632864165FCA4920
46548.pygtex [356])
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C0717BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C37BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B49407915BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BFBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704
\OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 
val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec
ted_frequencies[^^MD^^M, ^^ME^^M]

(./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF74BD02851C2FB632864165FCA4920
46548.pygtex [357])
(./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4FBD02851C2FB632864165FCA4920
46548.pygtex)) [358] (./Tutorial/chapter_testing.tex
Chapter 21.

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD062144BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0444BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907344BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D44BBF456F55B5DC060035246D76
9EADB.pygtex)
Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77
[]\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte
st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT
1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase
[359]
(./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED44BBF456F55B5DC060035246D76
9EADB.pygtex [360])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A79543DFECA235A69AE23006BA05B
4EB70.pygtex) [361]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706E9543DFECA235A69AE23006BA05B
4EB70.pygtex [362])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F444BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA299543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B82977119543DFECA235A69AE23006BA05B
4EB70.pygtex [363])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76
9EADB.pygtex) [364]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345644BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4344BBF456F55B5DC060035246D76
9EADB.pygtex)) [365] (./Tutorial/chapter_contributing.tex
Chapter 22.
[366]
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3644BBF456F55B5DC060035246D76
9EADB.pygtex) [367]) [368] (./Tutorial/chapter_appendix.tex
Chapter 23.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D32BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A4628599543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B429543DFECA235A69AE23006BA05B
4EB70.pygtex [369])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C429543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A203BD02851C2FB632864165FCA4920
46548.pygtex)) [370] [371] [372] [373] (./Tutorial.aux
(./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux)
(./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux)
(./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux)
(./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux)
(./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux)
(./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux)
(./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux)
(./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux)
(./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux)
(./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux)
(./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux)
(./Tutorial/chapter_appendix.aux))

LaTeX Warning: There were undefined references.


LaTeX Warning: There were multiply-defined labels.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb
xti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmitt10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmr5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on Tutorial.pdf (374 pages, 3024629 bytes).
Transcript written on Tutorial.log.
pdflatex --shell-escape "\def\bpversion{1.81}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2023-06-01> patch level 1
L3 programming layer <2023-08-29>
(./Tutorial.tex (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty)
(/usr/share/texmf/tex/latex/misc/hevea.sty
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') Excluding comment 'rawhtml'
Excluding comment 'htmlonly')
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/lineno/lineno.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/shellesc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/ifplatform/ifplatform.sty
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))
(/usr/share/texlive/texmf-dist/tex/generic/catchfile/catchfile.sty
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty))
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty) (./Tutorial.w18)
) (/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.sty
(/usr/share/texlive/texmf-dist/tex/generic/xstring/xstring.tex))
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 70.

(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))/usr/bin/pygmentize

(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./Tutorial.aux (./Tutorial/chapter_introduction.aux)
(./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux)
(./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux)
(./Tutorial/chapter_align.aux

LaTeX Warning: Label `sec:pairwise-general-gapscores' multiply defined.

) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux)
(./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux)
(./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux)
(./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux)
(./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux)
(./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux)
(./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux)
(./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux)
(./Tutorial/chapter_appendix.aux))
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(./Tutorial.out) (./Tutorial.out) Excluding 'htmlonly' comment.
Excluding 'rawhtml' comment. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.m
ap} <./images/biopython_logo.pdf>] (./Tutorial.toc
pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has 
been already used, duplicate ignored
<to be read again> 
                   \relax 
l.39 ...tions and locations}{37}{subsection.4.3.2}
                                                  % [1] [2] [3] [4] [5]
[6] [7]) [8] (./Tutorial/chapter_introduction.tex
Chapter 1.
[9] [10] Excluding 'rawhtml' comment.
Underfull \hbox (badness 10000) in paragraph at lines 122--128


Underfull \hbox (badness 10000) in paragraph at lines 134--136

(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/C3217FD04973F24516F5530BB525A22CBD02851C2FB632864165FCA4920
46548.pygtex) [11 <./images/biopython_logo_old.jpg>]
Overfull \hbox (2.99303pt too wide) in paragraph at lines 187--189
\OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor
t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or
 see [][]$\OT1/cmtt/m/n/10 http : / / biopython .
[12]) [13] (./Tutorial/chapter_quick_start.tex
Chapter 2.

LaTeX Warning: Reference `chapter:advanced' on page 14 undefined on input line 
14.


(./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612CBD02851C2FB632864165FCA4920
46548.pygtex [14])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535ABBD02851C2FB632864165FCA4920
46548.pygtex) [15]
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B0213346781855BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26DBD02851C2FB632864165FCA4920
46548.pygtex [16])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F2BD02851C2FB632864165FCA4920
46548.pygtex) [17]) [18] (./Tutorial/chapter_seq_objects.tex
Chapter 3.

(./_minted-Tutorial/048D805D0CE39D0271B0A9A9F6FA0B90BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDCBD02851C2FB632864165FCA4920
46548.pygtex) [19]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0F44B540F3531194878FC29AF017902BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E97622504BD02851C2FB632864165FCA4920
46548.pygtex [20])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E36BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D9386420BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/732D927996C79742AC990312B3D6EEB0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C270BD02851C2FB632864165FCA4920
46548.pygtex [21])
(./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC47BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D394BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8DBD02851C2FB632864165FCA4920
46548.pygtex [22])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF17BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC0BD02851C2FB632864165FCA4920
46548.pygtex [23])
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C8753BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B386BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A70BD02851C2FB632864165FCA4920
46548.pygtex [24])
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF82BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD64BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF98BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE79BD02851C2FB632864165FCA4920
46548.pygtex [25])
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B55990BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874DBD02851C2FB632864165FCA4920
46548.pygtex [26])
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/06DBC59F2EAD33E7A951888537876615BD02851C2FB632864165FCA4920
46548.pygtex) [27]
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C338BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CB669566ECC2CFEDC7429F829576A
D0DC6.pygtex [28])
(./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E84BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DFDB859800920408E228736AD921B5DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B040BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE451BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2EBD02851C2FB632864165FCA4920
46548.pygtex [29])
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C0BD02851C2FB632864165FCA4920
46548.pygtex)) [30] [31] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

(./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC809BD02851C2FB632864165FCA4920
46548.pygtex) [32]
(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D407BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC2BD02851C2FB632864165FCA4920
46548.pygtex [33])
(./_minted-Tutorial/510764EE0BB38AD6C688E71989677507669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D849822BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD2085BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9669566ECC2CFEDC7429F829576A
D0DC6.pygtex [34])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA601BD02851C2FB632864165FCA4920
46548.pygtex [35])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F926BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0DBD02851C2FB632864165FCA4920
46548.pygtex) [36] [37]
(./_minted-Tutorial/AD47AD29D6F7927F9406BE5609676388BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F3BD02851C2FB632864165FCA4920
46548.pygtex [38])
(./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D86C559003980DC8749AF92530435DFDBD02851C2FB632864165FCA4920
46548.pygtex) [39]
(./_minted-Tutorial/1C0A562378DEEE8E210765437B3E1700BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B49BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C75BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0C3ED75879971F09D72A92585654A32CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E3920BD02851C2FB632864165FCA4920
46548.pygtex [40])
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F9689BD02851C2FB632864165FCA4920
46548.pygtex [41])
(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B2340BD02851C2FB632864165FCA4920
46548.pygtex [42])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEBBD02851C2FB632864165FCA4920
46548.pygtex [43])
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A85BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B311BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D2457BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF82BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDFBD02851C2FB632864165FCA4920
46548.pygtex [44])
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF1718501669BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1BBD02851C2FB632864165FCA4920
46548.pygtex [45])
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED36BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E7BD02851C2FB632864165FCA4920
46548.pygtex) [46]
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B63BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B8793BD02851C2FB632864165FCA4920
46548.pygtex)) [47] (./Tutorial/chapter_seqio.tex
Chapter 5.

(./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D498BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB6789543DFECA235A69AE23006BA05B
4EB70.pygtex [48])
(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE5009549543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F19543DFECA235A69AE23006BA05B
4EB70.pygtex [49])
(./_minted-Tutorial/C82398A4A04383A063D2E648811230529543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [50]
(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD1622219543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD829543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE6BD02851C2FB632864165FCA4920
46548.pygtex [51])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E734519543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9562C263804C6DD613F075A435553A9FBD02851C2FB632864165FCA4920
46548.pygtex [52])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C91BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/23394A4616015FFE4619934E98424178BD02851C2FB632864165FCA4920
46548.pygtex [53])
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C09BD02851C2FB632864165FCA4920
46548.pygtex) [54]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD4769543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD89543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D79543DFECA235A69AE23006BA05B
4EB70.pygtex [55])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A49543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989FBD02851C2FB632864165FCA4920
46548.pygtex [56])
(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB03BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF6BD02851C2FB632864165FCA4920
46548.pygtex [57])
(./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/55430EAFE498E385842834603E0B8C869543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB89543DFECA235A69AE23006BA05B
4EB70.pygtex [58])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C178893BD02851C2FB632864165FCA4920
46548.pygtex) [59]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C78BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF4065BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A364BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D669543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CEBD02851C2FB632864165FCA4920
46548.pygtex [60])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853
\OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org /
 pub / databases / uniprot / current _ release / knowledgebase / complete /

(./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929DBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894
[]\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u
p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1
/cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C144BBF456F55B5DC060035246D76
9EADB.pygtex [61])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41044BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A2777BD02851C2FB632864165FCA4920
46548.pygtex) [62]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C6471BD02851C2FB632864165FCA4920
46548.pygtex) [63]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD73429543DFECA235A69AE23006BA05B
4EB70.pygtex [64])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4669566ECC2CFEDC7429F829576A
D0DC6.pygtex [65])
(./_minted-Tutorial/C194E2231D844AE7D0223173D2A899919543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEABD02851C2FB632864165FCA4920
46548.pygtex) [66]
(./_minted-Tutorial/920133226A22EEB682D854077D7FB78FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C260028BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E381FF526AC999B71717F178C997F6B2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26ABD02851C2FB632864165FCA4920
46548.pygtex) [67]
(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F539543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351
\OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) 
[]\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm
tt/m/n/10 SeqRecord.format(...)
[68]
(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397
[]\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm
tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt
/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D749A84299CF58E876E9A899069830DB9543DFECA235A69AE23006BA05B
4EB70.pygtex)) [69] (./Tutorial/chapter_align.tex
Chapter 6.

(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42669566ECC2CFEDC7429F829576A
D0DC6.pygtex [70])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AECBD02851C2FB632864165FCA4920
46548.pygtex [71])
(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A31077BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [72]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C560407BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533669566ECC2CFEDC7429F829576A
D0DC6.pygtex [73])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF756BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [74]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020669566ECC2CFEDC7429F829576A
D0DC6.pygtex [75])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [76]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D318BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477669566ECC2CFEDC7429F829576A
D0DC6.pygtex [77])
Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435
\OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t
or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()

Overfull \hbox (39.68698pt too wide) in paragraph at lines 442--447
[][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u
s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just
 use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert()

(./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F4024BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F669566ECC2CFEDC7429F829576A
D0DC6.pygtex [78])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99669566ECC2CFEDC7429F829576A
D0DC6.pygtex [79])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F169543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56669566ECC2CFEDC7429F829576A
D0DC6.pygtex [80])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2590B11C695B984E246A0A91734F786CBD02851C2FB632864165FCA4920
46548.pygtex) [81]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE5BD02851C2FB632864165FCA4920
46548.pygtex [82])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B71692BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB00BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E59BD02851C2FB632864165FCA4920
46548.pygtex [83])
(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A9253BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AE857C14E4731CC6F6EBA53051460097BD02851C2FB632864165FCA4920
46548.pygtex) [84]
(./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/523928538FA511A925EC995B1803BD16BD02851C2FB632864165FCA4920
46548.pygtex) [85]
(./_minted-Tutorial/CD47D1913C82182C164BD47DA4715282BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E893BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C63064BD02851C2FB632864165FCA4920
46548.pygtex) [86]
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A442BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F986368BD02851C2FB632864165FCA4920
46548.pygtex [87])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B045BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B27425BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130
[]\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi
le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO

(./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BDBD02851C2FB632864165FCA4920
46548.pygtex [88])
(./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F739998BD02851C2FB632864165FCA4920
46548.pygtex [89])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E7454BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5CBD02851C2FB632864165FCA4920
46548.pygtex [90])
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE74BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A240BD02851C2FB632864165FCA4920
46548.pygtex) [91]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/39152F199CEBB3375366F2E947824519BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF385674BD02851C2FB632864165FCA4920
46548.pygtex [92])
(./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE2493BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DF151703751D72BD556402B910190A87BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA88BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/554024580088332FAF0EA9296BACE82EBD02851C2FB632864165FCA4920
46548.pygtex) [93]
(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E361BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6CCC707502EDD92E9C355854215BF885BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C5BD02851C2FB632864165FCA4920
46548.pygtex [94])
(./_minted-Tutorial/E5E00F47BD7A0C8BC5F8818526283868BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE04BD02851C2FB632864165FCA4920
46548.pygtex) [95]
(./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/48453D528762FF183499778647AF218BBD02851C2FB632864165FCA4920
46548.pygtex [96])
(./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A39BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix
 []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu
tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt
t/m/n/10 aligner.mismatch_score

Overfull \hbox (47.73264pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 are ig-nored if [][]\OT1/cmtt/m/n/10 aligner.substitution_mat
rix []\OT1/cmr/m/n/10 is not [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . Set-t
ing [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 or [][]\OT1/cmtt
/m/n/10 aligner.mismatch_score

LaTeX Warning: `h' float specifier changed to `ht'.


Overfull \hbox (32.852pt too wide) in paragraph at lines 1776--1820
[][]

(./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CEBD02851C2FB632864165FCA4920
46548.pygtex [97]) [98] [99]
(./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514ABD02851C2FB632864165FCA4920
46548.pygtex) [100]
(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE1911BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB8671BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EFBD02851C2FB632864165FCA4920
46548.pygtex [101])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D01BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9FBD02851C2FB632864165FCA4920
46548.pygtex [102])
(./_minted-Tutorial/0758643069FF669538B9540ECD26C94CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A34296592BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/76E331C5187C259B69198E91FC4AD112BD02851C2FB632864165FCA4920
46548.pygtex [103])
(./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD357BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966BBD02851C2FB632864165FCA4920
46548.pygtex [104])
(./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/66AABFA387595237A8CE2518915213F8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B15E737F9393063B641148640673D991BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B46BD02851C2FB632864165FCA4920
46548.pygtex [105])
(./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/874975627BAB24A36A35FD4C633D246DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BDBD02851C2FB632864165FCA4920
46548.pygtex [106])
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A7BD02851C2FB632864165FCA4920
46548.pygtex [107])
(./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/52868B2F44504455E4969FEF2614B63BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB94BD02851C2FB632864165FCA4920
46548.pygtex) [108]
(./_minted-Tutorial/E7E68A8851DEEE300947A0531513417DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF65BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA1733BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6502BA65433924876427DBB6013C1003BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FDBD02851C2FB632864165FCA4920
46548.pygtex [109])
(./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F1012BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA5077BD02851C2FB632864165FCA4920
46548.pygtex [110])
(./_minted-Tutorial/779C61444C54C1736794F4E11B0E326DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E105BD02851C2FB632864165FCA4920
46548.pygtex [111])
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA77BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF796600BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613
\OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments 
is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing
 [][]\OT1/cmtt/m/n/10 len(alignments)

(./_minted-Tutorial/F89522EF58FB067C6521C367C7134716BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE20BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9CBD02851C2FB632864165FCA4920
46548.pygtex [112])
(./_minted-Tutorial/882BD2544386DECA236BF25C7DD64857BD02851C2FB632864165FCA4920
46548.pygtex [113])
(./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA70BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A29BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/13D646E6B49807044DBDC43707A09846BD02851C2FB632864165FCA4920
46548.pygtex [114])
(./_minted-Tutorial/467CA50C36874E405E988587FEC07686BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E62BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A94C18D2207C354646F831D57FD85B35BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D8BD02851C2FB632864165FCA4920
46548.pygtex [115])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A73BD02851C2FB632864165FCA4920
46548.pygtex [116])
(./_minted-Tutorial/AAF53200644F4F68779FB844730087D3BD02851C2FB632864165FCA4920
46548.pygtex [117])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE06BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057DBD02851C2FB632864165FCA4920
46548.pygtex [118])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/842D73F66680850822D006857AE71FE7BD02851C2FB632864165FCA4920
46548.pygtex) [119]
(./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE3135BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7C466424D72F09AE5AACA884161416F9BD02851C2FB632864165FCA4920
46548.pygtex [120])
(./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA825278BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F680093BD02851C2FB632864165FCA4920
46548.pygtex [121])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315ECBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D86241664707BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5669566ECC2CFEDC7429F829576A
D0DC6.pygtex [122])
(./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/60D893638743BD147116D13E00593D6CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D669566ECC2CFEDC7429F829576A
D0DC6.pygtex [123])
(./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9EDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6DBD02851C2FB632864165FCA4920
46548.pygtex [124])
(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F2519BD02851C2FB632864165FCA4920
46548.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED0BD02851C2FB632864165FCA4920
46548.pygtex) [125]
(./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F120EF3444F3192D48657B4E52407017BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F2091BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5DBD02851C2FB632864165FCA4920
46548.pygtex [126])
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C71BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75ABD02851C2FB632864165FCA4920
46548.pygtex [127])) [128] (./Tutorial/chapter_blast.tex
Chapter 7.

Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46
[]\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas
t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs 
&
[129]
(./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4EBD02851C2FB632864165FCA4920
46548.pygtex [130])
(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920
46548.pygtex) [131]
(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE4792BD02851C2FB632864165FCA4920
46548.pygtex) [132]
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD08BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C204BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE5218004BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F40394BD02851C2FB632864165FCA4920
46548.pygtex [133])
(./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D238BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68259DF5B1930070C029D5A72D891A36BD02851C2FB632864165FCA4920
46548.pygtex [134])
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924669566ECC2CFEDC7429F829576A
D0DC6.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.

LaTeX Warning: Float too large for page by 32.27644pt on input line 481.

) [135] [136 <./images/BlastRecord.png>] [137 <./images/PSIBlastRecord.png>]
(./Tutorial/chapter_searchio.tex
Chapter 8.

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [138]
Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93
[][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle 
con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10
 HSPFragment

Overfull \hbox (8.43927pt too wide) in paragraph at lines 105--107
[][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files
 with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/
m/n/10 QueryResult

(./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FCBD02851C2FB632864165FCA4920
46548.pygtex [139])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B51955BD02851C2FB632864165FCA4920
46548.pygtex [140])
(./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/362861C831165FEA5413E0240053CD89BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE327BD02851C2FB632864165FCA4920
46548.pygtex [141])
(./_minted-Tutorial/FD9C81C098491598DBFB6208173BB575BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A03BD02851C2FB632864165FCA4920
46548.pygtex) [142]
(./_minted-Tutorial/0B914838010D3E86EC368E1702EB7253BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E619BD02851C2FB632864165FCA4920
46548.pygtex [143])
(./_minted-Tutorial/DDECA9EB99D9FA38003A52C176593072BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/578CBF904F35965EECFEC1FA694F0752BD02851C2FB632864165FCA4920
46548.pygtex [144])
(./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD64BD02851C2FB632864165FCA4920
46548.pygtex) [145]
(./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC6246863BD02851C2FB632864165FCA4920
46548.pygtex) [146]
(./_minted-Tutorial/A3385B945E43CC076FFA693B27681F05BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE573577BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B46BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD95BD02851C2FB632864165FCA4920
46548.pygtex [147])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD880444BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C787BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745
[]\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10
 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr
/m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment

(./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA12BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A3536909BD02851C2FB632864165FCA4920
46548.pygtex [148])
(./_minted-Tutorial/16771935702D6A2A9762A80A621013D8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/046FE550C51B323D1E952A27E126FE19BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A55E467518B2E0F936A232F0970B1037BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB2021BD02851C2FB632864165FCA4920
46548.pygtex [149])
(./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EEDBD02851C2FB632864165FCA4920
46548.pygtex [150])
(./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D33BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/758BAC7574A59544686354199D20892CBD02851C2FB632864165FCA4920
46548.pygtex) [151]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA9BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059
\OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT
1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like 
[][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F4BD02851C2FB632864165FCA4920
46548.pygtex) [152]
Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092
[]\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us
-ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt
/m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E9868BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE55BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DEBD02851C2FB632864165FCA4920
46548.pygtex) [153]
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170
[]\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 
also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic
h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse

(./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C176BD02851C2FB632864165FCA4920
46548.pygtex)) [154] (./Tutorial/chapter_entrez.tex
Chapter 9.
[155]
(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB5BD02851C2FB632864165FCA4920
46548.pygtex) [156]
(./_minted-Tutorial/7692669934D8ED6DEE1B8B6684745421BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA36BD02851C2FB632864165FCA4920
46548.pygtex [157])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C008BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FACBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F6BD02851C2FB632864165FCA4920
46548.pygtex [158])
(./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C68BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D50277BD02851C2FB632864165FCA4920
46548.pygtex) [159]
(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19FBD02851C2FB632864165FCA4920
46548.pygtex) [160]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F3147BD02851C2FB632864165FCA4920
46548.pygtex [161] [162])
(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D59543DFECA235A69AE23006BA05B
4EB70.pygtex [163])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F487BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF008BD02851C2FB632864165FCA4920
46548.pygtex [164])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/68622353B578A611D2F621023E3C4BD1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F70BD02851C2FB632864165FCA4920
46548.pygtex [165])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC38BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0944BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722ABD02851C2FB632864165FCA4920
46548.pygtex [166])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF38669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0BBD02851C2FB632864165FCA4920
46548.pygtex [167])
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B669566ECC2CFEDC7429F829576A
D0DC6.pygtex [168])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6EF35C66998219AA15568E5FA366261EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD3676C48A9629929A55320028B512E5BD02851C2FB632864165FCA4920
46548.pygtex [169])
(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD669566ECC2CFEDC7429F829576A
D0DC6.pygtex [170])
(./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC12BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D75BD02851C2FB632864165FCA4920
46548.pygtex [171])
(./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E277BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A1266BD02851C2FB632864165FCA4920
46548.pygtex [172])
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019669566ECC2CFEDC7429F829576A
D0DC6.pygtex [173])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B624BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA5BD02851C2FB632864165FCA4920
46548.pygtex) [174]
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA19543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1EBD02851C2FB632864165FCA4920
46548.pygtex [175])
(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/964257041BEB9E732FF9A943209BD6EDBD02851C2FB632864165FCA4920
46548.pygtex [176])
(./_minted-Tutorial/600193D5D5D44162E61A3CAB40448426BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B642038BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A1BD02851C2FB632864165FCA4920
46548.pygtex [177])
(./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FDBD02851C2FB632864165FCA4920
46548.pygtex [178])
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A72797BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB3848BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D76169664531538D144C55FFC33571BBD02851C2FB632864165FCA4920
46548.pygtex) [179]
(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C45BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB93649BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D8BD02851C2FB632864165FCA4920
46548.pygtex) [180]
(./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C477BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E24BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F9633BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D5749543DFECA235A69AE23006BA05B
4EB70.pygtex [181])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA9543DFECA235A69AE23006BA05B
4EB70.pygtex) [182]
(./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927ABD02851C2FB632864165FCA4920
46548.pygtex)) [183] (./Tutorial/chapter_uniprot.tex
Chapter 10.

(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A86BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A668BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD6768BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/930B60BD569CAAF368B0E614553F3030BD02851C2FB632864165FCA4920
46548.pygtex) [184]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA6519182BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB934669BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD69228BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D14BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C06BD02851C2FB632864165FCA4920
46548.pygtex [185])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A4517918BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09ABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224669566ECC2CFEDC7429F829576A
D0DC6.pygtex [186])
(./_minted-Tutorial/956383F4066B9E093C9D2E3843CA0220BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307BBD02851C2FB632864165FCA4920
46548.pygtex [187])
(./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E2BD02851C2FB632864165FCA4920
46548.pygtex) [188]
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC783BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF9BD02851C2FB632864165FCA4920
46548.pygtex [189])
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B622BD02851C2FB632864165FCA4920
46548.pygtex [190])
Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366
[]\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n
/10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/
m/n/10 SwissProt.read(handle)

(./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87DBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410
[]\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m
en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re
cord

(./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B753BD02851C2FB632864165FCA4920
46548.pygtex) [191]
(./_minted-Tutorial/9457A436D281E066D350873A88476E59BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E7BD02851C2FB632864165FCA4920
46548.pygtex [192])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E86169BD02851C2FB632864165FCA4920
46548.pygtex)) [193] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C22853BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E69085BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C71BD02851C2FB632864165FCA4920
46548.pygtex [194])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA7388BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB35BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB8231BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879EBD02851C2FB632864165FCA4920
46548.pygtex) [195]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E18BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D176BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A024BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A5BD02851C2FB632864165FCA4920
46548.pygtex) [196]
(./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB136BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECECBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA4BD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264
\OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m
/n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato
m)
[197] Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D979BD02851C2FB632864165FCA4920
46548.pygtex) [198] [199 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD855BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB247BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E2727622BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A12BD02851C2FB632864165FCA4920
46548.pygtex) [200]
(./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DCBD02851C2FB632864165FCA4920
46548.pygtex) [201]
(./_minted-Tutorial/35E34E333445AAAA4E33570211335BA5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B1BD02851C2FB632864165FCA4920
46548.pygtex [202])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC88098BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB12492BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/76657140082404C594EE786B642215C3BD02851C2FB632864165FCA4920
46548.pygtex [203])
(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254CBD02851C2FB632864165FCA4920
46548.pygtex) [204]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB90BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B128BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B3BD02851C2FB632864165FCA4920
46548.pygtex [205])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF231899BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A624BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC2663BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA39BD02851C2FB632864165FCA4920
46548.pygtex [206])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E667BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899BBD02851C2FB632864165FCA4920
46548.pygtex [207])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AE729029ED6ABA2E38F17FAA1C60732CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8BB12A44CF293B1BF656E236EFE0BE12BD02851C2FB632864165FCA4920
46548.pygtex [208])
(./_minted-Tutorial/F0EFB999D116D041397B95C62B2EED29BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FE5531F727D4D28736FC18DF8A430EBBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E045C9432637E8C515E37CB4917FD57BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AD9DB5C434FCB2537E43EF340112BD08BD02851C2FB632864165FCA4920
46548.pygtex [209])
(./_minted-Tutorial/C1D5880B46A9CAEDCEB7F545F21B98CBBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (4.2397pt too wide) in paragraph at lines 1070--1074
\OT1/cmr/m/n/10 Missing atoms and other is-sues can cause prob-lems when re-bui
ld-ing a struc-ture. Use \OT1/cmtt/m/n/10 structure[]rebuild[]test$$

(./_minted-Tutorial/BD4323A41DFED2A7E4CD261AA65F95EDBD02851C2FB632864165FCA4920
46548.pygtex) [210]
(./_minted-Tutorial/6395F38A139598C6CC297CDBA73A8A43BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/21D2C13C2AA9395E0B1E4F1DDC801798BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/12E711A2CBFD0B046AA026208A117C1E9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/813FE78A3F8D8E46F06FF71539F000E69543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/CD78F368EB103F71947A3184BB62B46F9543DFECA235A69AE23006BA05B
4EB70.pygtex [211])
(./_minted-Tutorial/8E34478E945971E05C77F0A0E8C1B9D89543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/0D3FBB23D21A6A468370D56058193010BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BBA5405CCC4A3178ADA49DA358246C819543DFECA235A69AE23006BA05B
4EB70.pygtex [212])
(./_minted-Tutorial/DE601B1883F045FBEE1B28168CFF0CCABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AAF43F15691D49893FAEEAB7B7693A1D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/0ABBC5325B76EBCC5687BB33E7595F219543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment. [213 <./images/1a8o-ca-plot.png>]
Overfull \hbox (15.27203pt too wide) in paragraph at lines 1292--1295
[]\OT1/cmr/m/n/10 This work uses equa-tions de-vel-oped by Blue, the Hedronome-
ter, dis-cussed in [][]$\OT1/cmtt/m/n/10 https : / / math . stackexchange .

Overfull \hbox (116.15723pt too wide) in paragraph at lines 1292--1295
\OT1/cmtt/m/n/10 com / a / 49340 / 409$[][] \OT1/cmr/m/n/10 and fur-ther in [][
]$\OT1/cmtt/m/n/10 http : / / daylateanddollarshort . com / mathdocs / Heron-[]
like-[]Results-[]for-[]Tetrahedral-[]Volume .

(./_minted-Tutorial/BACD9263B6DB9FE9B9C8FA59C017D190BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2AECB4AED1E5DFDC387B42EF509CC3F4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1D3E5D8C6C6880A4C1D7DC0DEE7DC0C7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/815743EBD76EB14B6A71E1A4AE6433A4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B285099D410967E19F3165C7B5395544BD02851C2FB632864165FCA4920
46548.pygtex [214]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/5DFAFA7DE84292336F50FFB5DD8AD22A9543DFECA235A69AE23006BA05B
4EB70.pygtex [215 <./images/phe-pairs-3pbl.png>])
(./_minted-Tutorial/ED5201F27B6F2CC7A881AC419DF87B5E9543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (214.06847pt too wide) in paragraph at lines 1458--1474
[][] 
[216]
(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993CBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: Command \r invalid in math mode on input line 1527.


(./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705EBD02851C2FB632864165FCA4920
46548.pygtex [217])
(./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C6709BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/895E3343902EFB0E5475667B01C4B691BD02851C2FB632864165FCA4920
46548.pygtex [218]) [219]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB15BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A9BD02851C2FB632864165FCA4920
46548.pygtex [220])
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A74BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5DBD02851C2FB632864165FCA4920
46548.pygtex) [221]) [222] (./Tutorial/chapter_popgen.tex
Chapter 12.

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6B9543DFECA235A69AE23006BA05B
4EB70.pygtex) [223]
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC9543DFECA235A69AE23006BA05B
4EB70.pygtex)) [224] (./Tutorial/chapter_phylo.tex
Chapter 13.

(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15844BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C24BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4ADBD02851C2FB632864165FCA4920
46548.pygtex [225])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920
46548.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBABD02851C2FB632864165FCA4920
46548.pygtex) [226]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1ADBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185
[]\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t
he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor

(./_minted-Tutorial/29624A9666C9430AABADF395148BBF27BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B9BD02851C2FB632864165FCA4920
46548.pygtex [227 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9BBD02851C2FB632864165FCA4920
46548.pygtex [228 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/456F5679DCD4FF740E7A110889D86573BD02851C2FB632864165FCA4920
46548.pygtex [229])
(./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F55BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D3BD02851C2FB632864165FCA4920
46548.pygtex [230])
(./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEEBD02851C2FB632864165FCA4920
46548.pygtex) Excluding 'htmlonly' comment. [231 <./images/phylo-draw-example.p
ng>]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486
\OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, 
[][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"})
[232]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537
[]\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, 
find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10
 ,
[233]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF69543DFECA235A69AE23006BA05B
4EB70.pygtex) [234]
Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707
[]\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter
-act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier .

(./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD8119BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095BBD02851C2FB632864165FCA4920
46548.pygtex) [235]
(./_minted-Tutorial/0702C9875263768417DD3ED2EF78755EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D2BD02851C2FB632864165FCA4920
46548.pygtex) [236]) [237] (./Tutorial/chapter_motifs.tex
Chapter 14.

(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486ABD02851C2FB632864165FCA4920
46548.pygtex [238])
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D03BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE75BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D177BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D257173BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/86717C2BCE65F41FCDB8652763165857BD02851C2FB632864165FCA4920
46548.pygtex [239])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F61243192022BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB2476BD02851C2FB632864165FCA4920
46548.pygtex) [240]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA669566ECC2CFEDC7429F829576A
D0DC6.pygtex [241])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECDBD02851C2FB632864165FCA4920
46548.pygtex [242])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3FBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C76BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92669566ECC2CFEDC7429F829576A
D0DC6.pygtex [243])
(./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F706BD02851C2FB632864165FCA4920
46548.pygtex [244])
(./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DCBD02851C2FB632864165FCA4920
46548.pygtex [245])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FDBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFDBD02851C2FB632864165FCA4920
46548.pygtex [246])
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C378BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6BBD02851C2FB632864165FCA4920
46548.pygtex [247])
(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44669566ECC2CFEDC7429F829576A
D0DC6.pygtex [248])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909FBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606
\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man
d reads the com-plete file di-rectly, so you can close the file af-ter call-ing
 [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B84BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB6BD02851C2FB632864165FCA4920
46548.pygtex [249])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E012053BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7669566ECC2CFEDC7429F829576A
D0DC6.pygtex [250])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5CBD02851C2FB632864165FCA4920
46548.pygtex)

LaTeX Warning: `h' float specifier changed to `ht'.

[251]
(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EFBD02851C2FB632864165FCA4920
46548.pygtex [252])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F26406BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF51495BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE70605BD02851C2FB632864165FCA4920
46548.pygtex [253])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C74BD02851C2FB632864165FCA4920
46548.pygtex [254])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C98812BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E225BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F21BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E48BD02851C2FB632864165FCA4920
46548.pygtex [255])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7BBD02851C2FB632864165FCA4920
46548.pygtex [256])
(./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A81BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA161BD02851C2FB632864165FCA4920
46548.pygtex) [257]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E25BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A5092BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA2BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C86073BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE970BD02851C2FB632864165FCA4920
46548.pygtex [258])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E5BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF4BD02851C2FB632864165FCA4920
46548.pygtex [259])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E322BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C9BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD7261603BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA2473BD02851C2FB632864165FCA4920
46548.pygtex [260])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C1BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA16BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D3BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D3BD02851C2FB632864165FCA4920
46548.pygtex) [261]
(./_minted-Tutorial/868ABF9ABD2736A12F423306646D7706BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/912C817861E626118AB2FA06F12910B6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A26BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472669566ECC2CFEDC7429F829576A
D0DC6.pygtex) [262]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB41BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B6BD02851C2FB632864165FCA4920
46548.pygtex) [263]) [264] (./Tutorial/chapter_cluster.tex
Chapter 15.
[265] [266] [267] [268]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED4140BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C2B72A7408C7DF74DFCEBE0485997287BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE601735827BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A25009543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C0BD02851C2FB632864165FCA4920
46548.pygtex [269])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246
\OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra
nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$

(./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB34BD02851C2FB632864165FCA4920
46548.pygtex) [270] [271]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762EBD02851C2FB632864165FCA4920
46548.pygtex) [272]
(./_minted-Tutorial/C286E2777B917B774560CBDC7CF92626BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B
4EB70.pygtex) [273] [274]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424
[][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them.
 The items be-ing clus-tered are num-bered from 0 to $[]$,

(./_minted-Tutorial/015798D317E9D8732518AFD186C997CABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C239049267861739BD02851C2FB632864165FCA4920
46548.pygtex) [275]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F6BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203ADBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE22BD02851C2FB632864165FCA4920
46548.pygtex) [276]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F72BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D41BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF8895055BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEBBD02851C2FB632864165FCA4920
46548.pygtex [277])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED189543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC9543DFECA235A69AE23006BA05B
4EB70.pygtex) [278]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C175BD02851C2FB632864165FCA4920
46548.pygtex) [279]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEABD02851C2FB632864165FCA4920
46548.pygtex) [280]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABABBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961CBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750
 [] 
[281] [282]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F7BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAFBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FCBD02851C2FB632864165FCA4920
46548.pygtex) [283]
(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E0BD02851C2FB632864165FCA4920
46548.pygtex [284])
(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA8504BD02851C2FB632864165FCA4920
46548.pygtex) [285]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D70BD02851C2FB632864165FCA4920
46548.pygtex [286])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF58BD02851C2FB632864165FCA4920
46548.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116
[]\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result
_K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT
1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 
. 
[287] (./Tutorial/chapter_learning.tex
Chapter 16.
[288]
(./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4DBD02851C2FB632864165FCA4920
46548.pygtex [289])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4FBD02851C2FB632864165FCA4920
46548.pygtex [290])
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB096BD02851C2FB632864165FCA4920
46548.pygtex [291])
(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CEBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D402BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A012BD02851C2FB632864165FCA4920
46548.pygtex [292])

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 267.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 267.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 275.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 275.


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E6BD02851C2FB632864165FCA4920
46548.pygtex) [293]

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 287.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 287.


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA595BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B38BF6A3D910590D450B331A075B723CBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9BBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC1BD02851C2FB632864165FCA4920
46548.pygtex [294])
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC15BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A586FFDD9483C890754DBE5DFC420710BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D35BD02851C2FB632864165FCA4920
46548.pygtex [295])) [296] (./Tutorial/chapter_graphics.tex
Chapter 17.
[297]
(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A09543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D8169543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B0359543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA79543DFECA235A69AE23006BA05B
4EB70.pygtex [298]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E9543DFECA235A69AE23006BA05B
4EB70.pygtex [299 <./images/plasmid_linear.png (PNG copy)>]) [300 <./images/pla
smid_circular.png (PNG copy)>]
(./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF279543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A7359543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D8509543DFECA235A69AE23006BA05B
4EB70.pygtex [301]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B949543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C9543DFECA235A69AE23006BA05B
4EB70.pygtex [302] [303 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/67B3F646AA5F8690151428081229D39B9543DFECA235A69AE23006BA05B
4EB70.pygtex [304] [305 <./images/GD_sigils.png>] [306 <./images/GD_sigil_arrow
_shafts.png>] [307 <./images/GD_sigil_arrow_heads.png>] [308])
Excluding 'htmlonly' comment. [309 <./images/plasmid_linear_nice.png (PNG copy)
>] [310 <./images/plasmid_circular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA899543DFECA235A69AE23006BA05B
4EB70.pygtex [311])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177A9543DFECA235A69AE23006BA05B
4EB70.pygtex [312]) Excluding 'htmlonly' comment. [313 <./images/three_track_si
mple.png>]
(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA1119543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB9543DFECA235A69AE23006BA05B
4EB70.pygtex [314])
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD18409543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C289543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (2.65141pt too wide) in paragraph at lines 873--879
[]\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the
 [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm
tt/m/n/10 cross_track_links
Excluding 'htmlonly' comment. [315] Excluding 'htmlonly' comment. [316 <./image
s/three_track_cl.png>] [317 <./images/three_track_cl2a.png>]
(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F7284149779543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F9543DFECA235A69AE23006BA05B
4EB70.pygtex) [318]
(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C9543DFECA235A69AE23006BA05B
4EB70.pygtex [319] [320 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A759543DFECA235A69AE23006BA05B
4EB70.pygtex [321]) Excluding 'htmlonly' comment.) [322]
(./Tutorial/chapter_kegg.tex
Chapter 18.

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4ABD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C71BD02851C2FB632864165FCA4920
46548.pygtex) [323]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B9543DFECA235A69AE23006BA05B
4EB70.pygtex [324])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95669566ECC2CFEDC7429F829576A
D0DC6.pygtex)) [325] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8DBD02851C2FB632864165FCA4920
46548.pygtex) [326]
(./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA9721BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB44BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB081BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159EBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF8BD02851C2FB632864165FCA4920
46548.pygtex [327])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51DBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D7206BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579DBD02851C2FB632864165FCA4920
46548.pygtex [328])
(./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E0872188BD02851C2FB632864165FCA4920
46548.pygtex [329])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E6BD02851C2FB632864165FCA4920
46548.pygtex)) [330] (./Tutorial/chapter_cookbook.tex
Chapter 20.

(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB9543DFECA235A69AE23006BA05B
4EB70.pygtex [331])
(./_minted-Tutorial/CA0835D76EF6887731674D8AB555091B9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A0BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E57164BD02851C2FB632864165FCA4920
46548.pygtex) [332]
(./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD4BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54F9543DFECA235A69AE23006BA05B
4EB70.pygtex [333])
(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F649543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A02396470619543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B9543DFECA235A69AE23006BA05B
4EB70.pygtex [334])
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC655419543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE4087939543DFECA235A69AE23006BA05B
4EB70.pygtex) [335]
(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA29543DFECA235A69AE23006BA05B
4EB70.pygtex) [336]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF6418319543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F354509543DFECA235A69AE23006BA05B
4EB70.pygtex)
Overfull \hbox (5.83499pt too wide) in paragraph at lines 454--458
\OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul
d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/AB16E58608A2F17CC79E6929557208879543DFECA235A69AE23006BA05B
4EB70.pygtex [337])
Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477
\OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849.
fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[
]primer.fastq\OT1/cmr/m/n/10 . 

(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA5569543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A9543DFECA235A69AE23006BA05B
4EB70.pygtex [338])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C9543DFECA235A69AE23006BA05B
4EB70.pygtex) [339]
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F89159543DFECA235A69AE23006BA05B
4EB70.pygtex) [340]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C319543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC407373679543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D2587BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B69543DFECA235A69AE23006BA05B
4EB70.pygtex [341])
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B59543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A09543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582EBD02851C2FB632864165FCA4920
46548.pygtex [342])
(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB80BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEBBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7DBD02851C2FB632864165FCA4920
46548.pygtex [343])
(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B8BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF098BD02851C2FB632864165FCA4920
46548.pygtex) [344]
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B29543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052669566ECC2CFEDC7429F829576A
D0DC6.pygtex [345])
(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CCBD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B79543DFECA235A69AE23006BA05B
4EB70.pygtex [346]) Excluding 'htmlonly' comment.
Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120
[]\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10
 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use
 [][]\OT1/cmtt/m/n/10 pylab.savefig(...)

(./_minted-Tutorial/798776F436EA559BACD9C305C09973919543DFECA235A69AE23006BA05B
4EB70.pygtex [347 <./images/hist_plot.png>])
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
[348 <./images/gc_plot.png>]
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF79543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/80A47C8780CE3021D53829563E8166569543DFECA235A69AE23006BA05B
4EB70.pygtex [349 <./images/dot_plot.png>])
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F49543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B39543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/6655B5CD97C33186A22E6897501301FF9543DFECA235A69AE23006BA05B
4EB70.pygtex [350])
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD9543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment. [351 <./images/dot_plot_scatter.png
>]
(./_minted-Tutorial/601CCA4B782F1DA528DB81B0248031959543DFECA235A69AE23006BA05B
4EB70.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC739543DFECA235A69AE23006BA05B
4EB70.pygtex) [352]
(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA39543DFECA235A69AE23006BA05B
4EB70.pygtex) [353 <./images/SRR001666.png>]
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA48145359543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529
[]\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l
ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c
mr/m/n/10 .

(./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFFBD02851C2FB632864165FCA4920
46548.pygtex [354])
(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB5300659543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A409543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D0439543DFECA235A69AE23006BA05B
4EB70.pygtex [355])
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C9543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C973BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FABD02851C2FB632864165FCA4920
46548.pygtex [356])
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C0717BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C37BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B49407915BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BFBD02851C2FB632864165FCA4920
46548.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704
\OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 
val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec
ted_frequencies[^^MD^^M, ^^ME^^M]

(./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF74BD02851C2FB632864165FCA4920
46548.pygtex [357])
(./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4FBD02851C2FB632864165FCA4920
46548.pygtex)) [358] (./Tutorial/chapter_testing.tex
Chapter 21.

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD062144BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0444BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907344BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D44BBF456F55B5DC060035246D76
9EADB.pygtex)
Overfull \hbox (39.35472pt too wide) in paragraph at lines 73--77
[]\OT1/cmr/m/n/10 Tests based on Python's stan-dard [][]\OT1/cmtt/m/n/10 unitte
st []\OT1/cmr/m/n/10 frame-work will [][]\OT1/cmtt/m/n/10 import unittest []\OT
1/cmr/m/n/10 and then de-fine [][]\OT1/cmtt/m/n/10 unittest.TestCase
[359]
(./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64669566ECC2CFEDC7429F829576A
D0DC6.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED44BBF456F55B5DC060035246D76
9EADB.pygtex [360])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A79543DFECA235A69AE23006BA05B
4EB70.pygtex) [361]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB99543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD44BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706E9543DFECA235A69AE23006BA05B
4EB70.pygtex [362])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F444BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA299543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B82977119543DFECA235A69AE23006BA05B
4EB70.pygtex [363])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F44BBF456F55B5DC060035246D76
9EADB.pygtex) [364]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345644BBF456F55B5DC060035246D76
9EADB.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4344BBF456F55B5DC060035246D76
9EADB.pygtex)) [365] (./Tutorial/chapter_contributing.tex
Chapter 22.
[366]
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3644BBF456F55B5DC060035246D76
9EADB.pygtex) [367]) [368] (./Tutorial/chapter_appendix.tex
Chapter 23.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D32BD02851C2FB632864165FCA4920
46548.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A4628599543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B429543DFECA235A69AE23006BA05B
4EB70.pygtex [369])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C429543DFECA235A69AE23006BA05B
4EB70.pygtex)
(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A203BD02851C2FB632864165FCA4920
46548.pygtex)) [370] [371] [372] [373] (./Tutorial.aux
(./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux)
(./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux)
(./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux)
(./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux)
(./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux)
(./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux)
(./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux)
(./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux)
(./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux)
(./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux)
(./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux)
(./Tutorial/chapter_appendix.aux))

LaTeX Warning: There were undefined references.


LaTeX Warning: There were multiply-defined labels.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb
xti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmitt10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmr5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on Tutorial.pdf (374 pages, 3024630 bytes).
Transcript written on Tutorial.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2023-06-01> patch level 1
L3 programming layer <2023-08-29>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 56.

(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf))
(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file biopdb_faq.aux.
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: a4paper
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: 
* h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt)
* v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt)
* \paperwidth=597.50787pt
* \paperheight=845.04684pt
* \textwidth=418.25368pt
* \textheight=731.23584pt
* \oddsidemargin=17.3571pt
* \evensidemargin=17.3571pt
* \topmargin=-52.36449pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=10.0pt
* \footskip=30.0pt
* \marginparwidth=65.0pt
* \marginparsep=11.0pt
* \columnsep=10.0pt
* \skip\footins=9.0pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidefalse
* \@mparswitchfalse
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119
[]\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p
bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-
dist/fonts/enc/dvips/base/8r.enc}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2]
Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276
\T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in 
the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 ,
[3]
Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318
\T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d
ate, release_-date, structure_-

Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318
\T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to
 a list of ref-er-ences), \T1/pcr/m/n/10 journal_-

LaTeX Warning: Reference `sub:The-Structure-object' on page 4 undefined on inpu
t line 335.

[4] [5]

LaTeX Warning: Reference `cap:SMCRA' on page 6 undefined on input line 548.

[6] [7 <./images/smcra.png (PNG copy)>] [8]

LaTeX Warning: Reference `cap:SMCRA' on page 9 undefined on input line 750.


LaTeX Warning: Reference `cap:SMCRA' on page 9 undefined on input line 779.


LaTeX Warning: Reference `sub:Analysis' on page 9 undefined on input line 821.

[9]

LaTeX Warning: Reference `sub:Analysis' on page 10 undefined on input line 826.


[10]
Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016
\T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co
n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 .

Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024
\T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob-
tained from the \T1/pcr/m/n/10 Polypeptide
[11]

LaTeX Warning: Reference `cap:DSSP-codes' on page 12 undefined on input line 10
41.

[12]
Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149
[]\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e
xposure(model)  

Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174
\T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1
/pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m
/n/10 get_vector
[13] [14]
Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353
[]\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE 
DIS-CLAIM
[15] (./biopdb_faq.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.


Package rerunfilecheck Warning: File `biopdb_faq.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/bookman/ubkd8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookma
n/ubkl8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkli8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/
texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf
-dist/fonts/type1/urw/courier/ucrro8a.pfb>
Output written on biopdb_faq.pdf (15 pages, 163591 bytes).
Transcript written on biopdb_faq.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2023-06-01> patch level 1
L3 programming layer <2023-08-29>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 56.

(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf))
(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./biopdb_faq.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: a4paper
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: 
* h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt)
* v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt)
* \paperwidth=597.50787pt
* \paperheight=845.04684pt
* \textwidth=418.25368pt
* \textheight=731.23584pt
* \oddsidemargin=17.3571pt
* \evensidemargin=17.3571pt
* \topmargin=-52.36449pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=10.0pt
* \footskip=30.0pt
* \marginparwidth=65.0pt
* \marginparsep=11.0pt
* \columnsep=10.0pt
* \skip\footins=9.0pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidefalse
* \@mparswitchfalse
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))
(./biopdb_faq.out) (./biopdb_faq.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119
[]\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p
bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-
dist/fonts/enc/dvips/base/8r.enc}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2]
Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276
\T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in 
the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 ,
[3]
Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318
\T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d
ate, release_-date, structure_-

Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318
\T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to
 a list of ref-er-ences), \T1/pcr/m/n/10 journal_-
[4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10]
Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016
\T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co
n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 .

Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024
\T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob-
tained from the \T1/pcr/m/n/10 Polypeptide
[11] [12]
Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149
[]\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e
xposure(model)  

Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174
\T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1
/pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m
/n/10 get_vector
[13] [14]
Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353
[]\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE 
DIS-CLAIM
[15] (./biopdb_faq.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/bookman/ubkd8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookma
n/ubkl8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkli8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/
texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf
-dist/fonts/type1/urw/courier/ucrro8a.pfb>
Output written on biopdb_faq.pdf (15 pages, 165504 bytes).
Transcript written on biopdb_faq.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2023-06-01> patch level 1
L3 programming layer <2023-08-29>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 56.

(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf))
(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./biopdb_faq.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: a4paper
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: 
* h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt)
* v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt)
* \paperwidth=597.50787pt
* \paperheight=845.04684pt
* \textwidth=418.25368pt
* \textheight=731.23584pt
* \oddsidemargin=17.3571pt
* \evensidemargin=17.3571pt
* \topmargin=-52.36449pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=10.0pt
* \footskip=30.0pt
* \marginparwidth=65.0pt
* \marginparsep=11.0pt
* \columnsep=10.0pt
* \skip\footins=9.0pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidefalse
* \@mparswitchfalse
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))
(./biopdb_faq.out) (./biopdb_faq.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119
[]\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p
bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-
dist/fonts/enc/dvips/base/8r.enc}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pbk.fd) [2]
Overfull \hbox (21.75009pt too wide) in paragraph at lines 271--276
\T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in 
the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 ,
[3]
Overfull \hbox (13.9754pt too wide) in paragraph at lines 312--318
\T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d
ate, release_-date, structure_-

Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318
\T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to
 a list of ref-er-ences), \T1/pcr/m/n/10 journal_-
[4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10]
Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016
\T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co
n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 .

Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024
\T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob-
tained from the \T1/pcr/m/n/10 Polypeptide
[11] [12]
Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149
[]\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e
xposure(model)  

Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174
\T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1
/pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m
/n/10 get_vector
[13] [14]
Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353
[]\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE 
DIS-CLAIM
[15] (./biopdb_faq.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/bookman/ubkd8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookma
n/ubkl8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkli8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/
texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf
-dist/fonts/type1/urw/courier/ucrro8a.pfb>
Output written on biopdb_faq.pdf (15 pages, 165504 bytes).
Transcript written on biopdb_faq.log.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/Doc'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/python3-biopython.debhelper.log
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p Tests_avoid
for avoid in  PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth mmtf mmtf_online GraphicsBitmaps raxml_tool BioSQL_MySQLdb BioSQL_psycopg2   \
	    ; do \
    mv Tests/test_${avoid}.py Tests_avoid ; \
done
mv: cannot stat 'Tests/test_NACCESS_tool.py': No such file or directory
# For the doc package we need a clean testsuite without all the remaining files.  So keep a clean copy here
mkdir -p debian/tmp_tests
cp -a Tests debian/tmp_tests
# remove duplicated file
rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz
# We also keep the tests we need to avoid for later inspection
cp -a Tests_avoid debian/tmp_tests
# in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir
# to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set
LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
	--test-args='set -e; \
                             mkdir -p {build_dir}/home; \
                             mkdir -p {build_dir}/Doc/examples; \
                             cp -a Doc/Tutorial.tex {build_dir}/Doc; \
                             cp -a Doc/Tutorial {build_dir}/Doc; \
                             cp -a Doc/examples {build_dir}/Doc; \
                             cp -a Tests {build_dir}; \
                             cd {build_dir}/Tests; \
                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline'
	pybuild --test -i python{version} -p 3.11 --test --system=custom "--test-args=set -e; \\\
                             mkdir -p {build_dir}/home; \\\
                             mkdir -p {build_dir}/Doc/examples; \\\
                             cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\
                             cp -a Doc/Tutorial {build_dir}/Doc; \\\
                             cp -a Doc/examples {build_dir}/Doc; \\\
                             cp -a Tests {build_dir}; \\\
                             cd {build_dir}/Tests; \\\
                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline"
I: pybuild base:310: set -e; \
                             mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home; \
                             mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples; \
                             cp -a Doc/Tutorial.tex /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Doc/Tutorial /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Doc/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; \
                             cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests; \
                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home python3.11 run_tests.py --offline
test_Ace ... ok
test_Affy ... ok
test_AlignIO ... ok
test_AlignIO_ClustalIO ... ok
test_AlignIO_EmbossIO ... ok
test_AlignIO_FastaIO ... ok
test_AlignIO_MauveIO ... ok
test_AlignIO_PhylipIO ... ok
test_AlignIO_convert ... ok
test_AlignInfo ... ok
test_Align_Alignment ... ok
test_Align_a2m ... ok
test_Align_bed ... ok
test_Align_bigbed ... ok
test_Align_bigmaf ... ok
test_Align_bigpsl ... ok
test_Align_clustal ... ok
test_Align_emboss ... ok
test_Align_exonerate ... ok
test_Align_fasta ... ok
test_Align_hhr ... ok
test_Align_maf ... ok
test_Align_mauve ... ok
test_Align_msf ... ok
test_Align_nexus ... ok
test_Align_phylip ... ok
test_Align_psl ... ok
test_Align_sam ... ok
test_Align_stockholm ... ok
test_Align_tabular ... ok
test_Application ... ok
test_BWA_tool ... ok
test_BioSQL_MySQLdb_online ... skipping. internet not available
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
test_BioSQL_mysql_connector_online ... skipping. internet not available
test_BioSQL_psycopg2_online ... skipping. internet not available
test_BioSQL_sqlite3 ... ok
test_BioSQL_sqlite3_online ... skipping. internet not available
test_Blast_Record ... ok
test_CAPS ... ok
test_Chi2 ... ok
test_ClustalOmega_tool ... ok
test_Clustalw_tool ... ok
test_Cluster ... ok
test_CodonTable ... ok
test_ColorSpiral ... ok
test_Compass ... ok
test_Consensus ... ok
test_Dialign_tool ... ok
test_EMBL_unittest ... ok
test_Emboss ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_EmbossPrimer ... ok
test_Entrez ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/__init__.py:694: UserWarning: 
            Email address is not specified.

            To make use of NCBI's E-utilities, NCBI requires you to specify your
            email address with each request.  As an example, if your email address
            is A.N.Other@example.com, you can specify it as follows:
               from Bio import Entrez
               Entrez.email = 'A.N.Other@example.com'
            In case of excessive usage of the E-utilities, NCBI will attempt to contact
            a user at the email address provided before blocking access to the
            E-utilities.
  warnings.warn(
ok
test_Entrez_online ... skipping. internet not available
test_Entrez_parser ... ok
test_Enzyme ... ok
test_ExPASy ... skipping. internet not available
test_Fasttree_tool ... ok
test_File ... ok
test_GenBank ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica'
ok
test_GraphicsChromosome ... ok
test_GraphicsDistribution ... ok
test_GraphicsGeneral ... ok
test_HMMCasino ... ok
test_HMMGeneral ... ok
test_KEGG ... ok
test_KEGG_online ... skipping. internet not available
test_KGML_graphics ... ok
test_KGML_graphics_online ... skipping. internet not available
test_KGML_nographics ... ok
test_KeyWList ... ok
test_LogisticRegression ... ok
test_MafIO_index ... ok
test_Mafft_tool ... ok
test_MarkovModel ... ok
test_Medline ... ok
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
test_NCBITextParser ... ok
test_NCBIXML ... ok
test_NCBI_BLAST_tools ... ok
test_NCBI_qblast ... ok
test_NMR ... ok
test_NaiveBayes ... ok
test_Nexus ... ok
test_PAML_baseml ... ok
test_PAML_codeml ... ok
test_PAML_yn00 ... ok
test_PDBList ... skipping. internet not available
test_PDB_CEAligner ... ok
test_PDB_DSSP ... ok
test_PDB_Dice ... ok
test_PDB_Disordered ... ok
test_PDB_Exposure ... ok
test_PDB_FragmentMapper ... ok
test_PDB_KDTree ... ok
test_PDB_MMCIF2Dict ... ok
test_PDB_MMCIFIO ... ok
test_PDB_MMCIFParser ... ok
test_PDB_NACCESS ... ok
test_PDB_PDBIO ... ok
test_PDB_PDBParser ... ok
test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
test_PDB_Polypeptide ... ok
test_PDB_QCSuperimposer ... ok
test_PDB_SASA ... ok
test_PDB_SMCRA ... ok
test_PDB_Selection ... ok
test_PDB_StructureAlignment ... ok
test_PDB_Superimposer ... ok
test_PDB_internal_coords ... ok
test_PDB_parse_pdb_header ... ok
test_PDB_vectors ... ok
test_PQR ... ok
test_Pathway ... ok
test_Phd ... ok
test_Phylo ... ok
test_PhyloXML ... ok
test_Phylo_CDAO ... ok
test_Phylo_NeXML ... ok
test_Phylo_matplotlib ... ok
test_Phylo_networkx ... ok
test_PopGen_GenePop_nodepend ... ok
test_Prank_tool ... ok
test_Probcons_tool ... ok
test_ProtParam ... ok
test_RCSBFormats ... ok
test_Restriction ... ok
test_SCOP_Astral ... ok
test_SCOP_Cla ... ok
test_SCOP_Des ... ok
test_SCOP_Dom ... ok
test_SCOP_Hie ... ok
test_SCOP_Raf ... ok
test_SCOP_Residues ... ok
test_SCOP_Scop ... ok
test_SCOP_online ... skipping. internet not available
test_SVDSuperimposer ... ok
test_SearchIO_blast_tab ... ok
test_SearchIO_blast_tab_index ... ok
test_SearchIO_blast_text ... ok
test_SearchIO_blast_xml ... ok
test_SearchIO_blast_xml_index ... ok
test_SearchIO_blat_psl ... ok
test_SearchIO_blat_psl_index ... ok
test_SearchIO_exonerate ... ok
test_SearchIO_exonerate_text_index ... ok
test_SearchIO_exonerate_vulgar_index ... ok
test_SearchIO_fasta_m10 ... ok
test_SearchIO_fasta_m10_index ... ok
test_SearchIO_hhsuite2_text ... ok
test_SearchIO_hmmer2_text ... ok
test_SearchIO_hmmer2_text_index ... ok
test_SearchIO_hmmer3_domtab ... ok
test_SearchIO_hmmer3_domtab_index ... ok
test_SearchIO_hmmer3_tab ... ok
test_SearchIO_hmmer3_tab_index ... ok
test_SearchIO_hmmer3_text ... ok
test_SearchIO_hmmer3_text_index ... ok
test_SearchIO_interproscan_xml ... ok
test_SearchIO_legacy ... ok
test_SearchIO_model ... ok
test_SearchIO_write ... ok
test_SeqFeature ... ok
test_SeqIO ... ok
test_SeqIO_AbiIO ... ok
test_SeqIO_FastaIO ... ok
test_SeqIO_Gck ... ok
test_SeqIO_Insdc ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
  warnings.warn(
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_SeqIO_NibIO ... ok
test_SeqIO_PdbIO ... ok
test_SeqIO_QualityIO ... ok
test_SeqIO_SeqXML ... ok
test_SeqIO_SnapGene ... ok
test_SeqIO_TwoBitIO ... ok
test_SeqIO_Xdna ... ok
test_SeqIO_features ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
  warnings.warn(
ok
test_SeqIO_index ... ok
test_SeqIO_online ... skipping. internet not available
test_SeqIO_write ... ok
test_SeqRecord ... ok
test_SeqUtils ... ok
test_Seq_objs ... ok
test_SffIO ... ok
test_SwissProt ... ok
test_TCoffee_tool ... ok
test_TogoWS ... skipping. internet not available
test_TreeConstruction ... ok
test_Tutorial ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(
ok
test_UniGene ... ok
test_UniProt_GOA ... ok
test_Uniprot ... ok
test_Wise ... ok
test_align ... ok
test_align_substitution_matrices ... ok
test_bgzf ... ok
test_cellosaurus ... ok
test_codonalign ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython.
  warnings.warn(
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Seq.py:2779: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid.
  warnings.warn(
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
  warnings.warn(
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA)
  warnings.warn(
ok
test_geo ... ok
test_kNN ... ok
test_motifs ... ok
test_motifs_online ... skipping. internet not available
test_pairwise2 ... ok
test_pairwise2_no_C ... ok
test_pairwise_aligner ... ok
test_pairwise_alignment_map ... ok
test_phenotype ... ok
test_phenotype_fit ... ok
test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
test_prodoc ... ok
test_prosite ... ok
test_samtools_tool ... ok
test_seq ... ok
test_translate ... ok
Bio docstring test ... ok
Bio.Affy docstring test ... ok
Bio.Affy.CelFile docstring test ... ok
Bio.Align docstring test ... ok
Bio.Align.AlignInfo docstring test ... ok
Bio.Align.Applications docstring test ... ok
Bio.Align.Applications._ClustalOmega docstring test ... ok
Bio.Align.Applications._Clustalw docstring test ... ok
Bio.Align.Applications._Dialign docstring test ... ok
Bio.Align.Applications._MSAProbs docstring test ... ok
Bio.Align.Applications._Mafft docstring test ... ok
Bio.Align.Applications._Muscle docstring test ... ok
Bio.Align.Applications._Prank docstring test ... ok
Bio.Align.Applications._Probcons docstring test ... ok
Bio.Align.Applications._TCoffee docstring test ... ok
Bio.Align._aligners docstring test ... ok
Bio.Align.a2m docstring test ... ok
Bio.Align.bed docstring test ... ok
Bio.Align.bigbed docstring test ... ok
Bio.Align.bigmaf docstring test ... ok
Bio.Align.bigpsl docstring test ... ok
Bio.Align.clustal docstring test ... ok
Bio.Align.emboss docstring test ... ok
Bio.Align.exonerate docstring test ... ok
Bio.Align.fasta docstring test ... ok
Bio.Align.hhr docstring test ... ok
Bio.Align.interfaces docstring test ... ok
Bio.Align.maf docstring test ... ok
Bio.Align.mauve docstring test ... ok
Bio.Align.msf docstring test ... ok
Bio.Align.nexus docstring test ... ok
Bio.Align.phylip docstring test ... ok
Bio.Align.psl docstring test ... ok
Bio.Align.sam docstring test ... ok
Bio.Align.stockholm docstring test ... ok
Bio.Align.substitution_matrices docstring test ... ok
Bio.Align.tabular docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.ClustalIO docstring test ... ok
Bio.AlignIO.EmbossIO docstring test ... ok
Bio.AlignIO.FastaIO docstring test ... ok
Bio.AlignIO.Interfaces docstring test ... ok
Bio.AlignIO.MafIO docstring test ... ok
Bio.AlignIO.MauveIO docstring test ... ok
Bio.AlignIO.MsfIO docstring test ... ok
Bio.AlignIO.NexusIO docstring test ... ok
Bio.AlignIO.PhylipIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Application docstring test ... ok
Bio.Blast docstring test ... ok
Bio.Blast.Applications docstring test ... ok
Bio.Blast.NCBIWWW docstring test ... ok
Bio.Blast.NCBIXML docstring test ... ok
Bio.Blast.ParseBlastTable docstring test ... ok
Bio.Blast.Record docstring test ... ok
Bio.CAPS docstring test ... ok
Bio.Cluster docstring test ... ok
Bio.Cluster._cluster docstring test ... ok
Bio.Compass docstring test ... ok
Bio.Data docstring test ... ok
Bio.Data.CodonTable docstring test ... ok
Bio.Data.IUPACData docstring test ... ok
Bio.Data.PDBData docstring test ... ok
Bio.Data.SCOPData docstring test ... ok
Bio.Emboss docstring test ... ok
Bio.Emboss.Applications docstring test ... ok
Bio.Emboss.Primer3 docstring test ... ok
Bio.Emboss.PrimerSearch docstring test ... ok
Bio.Entrez.Parser docstring test ... ok
Bio.ExPASy.Enzyme docstring test ... ok
Bio.ExPASy.Prodoc docstring test ... ok
Bio.ExPASy.Prosite docstring test ... ok
Bio.ExPASy.ScanProsite docstring test ... ok
Bio.File docstring test ... ok
Bio.GenBank docstring test ... ok
Bio.GenBank.Record docstring test ... ok
Bio.GenBank.Scanner docstring test ... ok
Bio.GenBank.utils docstring test ... ok
Bio.Geo docstring test ... ok
Bio.Geo.Record docstring test ... ok
Bio.Graphics docstring test ... ok
Bio.Graphics.BasicChromosome docstring test ... ok
Bio.Graphics.ColorSpiral docstring test ... ok
Bio.Graphics.Comparative docstring test ... ok
Bio.Graphics.DisplayRepresentation docstring test ... ok
Bio.Graphics.Distribution docstring test ... ok
Bio.Graphics.GenomeDiagram docstring test ... ok
Bio.Graphics.GenomeDiagram._AbstractDrawer docstring test ... ok
Bio.Graphics.GenomeDiagram._CircularDrawer docstring test ... ok
Bio.Graphics.GenomeDiagram._Colors docstring test ... ok
Bio.Graphics.GenomeDiagram._CrossLink docstring test ... ok
Bio.Graphics.GenomeDiagram._Diagram docstring test ... ok
Bio.Graphics.GenomeDiagram._Feature docstring test ... ok
Bio.Graphics.GenomeDiagram._FeatureSet docstring test ... ok
Bio.Graphics.GenomeDiagram._Graph docstring test ... ok
Bio.Graphics.GenomeDiagram._GraphSet docstring test ... ok
Bio.Graphics.GenomeDiagram._LinearDrawer docstring test ... ok
Bio.Graphics.GenomeDiagram._Track docstring test ... ok
Bio.Graphics.KGML_vis docstring test ... ok
Bio.HMM docstring test ... ok
Bio.HMM.DynamicProgramming docstring test ... ok
Bio.HMM.MarkovModel docstring test ... ok
Bio.HMM.Trainer docstring test ... ok
Bio.HMM.Utilities docstring test ... ok
Bio.KEGG docstring test ... ok
Bio.KEGG.Compound docstring test ... ok
Bio.KEGG.Enzyme docstring test ... ok
Bio.KEGG.Gene docstring test ... ok
Bio.KEGG.KGML docstring test ... ok
Bio.KEGG.KGML.KGML_parser docstring test ... ok
Bio.KEGG.KGML.KGML_pathway docstring test ... ok
Bio.KEGG.Map docstring test ... ok
Bio.KEGG.REST docstring test ... ok
Bio.LogisticRegression docstring test ... ok
Bio.MarkovModel docstring test ... ok
Bio.MaxEntropy docstring test ... ok
Bio.Medline docstring test ... ok
Bio.NMR docstring test ... ok
Bio.NMR.NOEtools docstring test ... ok
Bio.NMR.xpktools docstring test ... ok
Bio.NaiveBayes docstring test ... ok
Bio.Nexus docstring test ... ok
Bio.Nexus.Nexus docstring test ... ok
Bio.Nexus.Nodes docstring test ... ok
Bio.Nexus.StandardData docstring test ... ok
Bio.Nexus.Trees docstring test ... ok
Bio.Nexus.cnexus docstring test ... ok
Bio.PDB docstring test ... ok
Bio.PDB.AbstractPropertyMap docstring test ... ok
Bio.PDB.Atom docstring test ... ok
Bio.PDB.Chain docstring test ... ok
Bio.PDB.DSSP docstring test ... ok
Bio.PDB.Dice docstring test ... ok
Bio.PDB.Entity docstring test ... ok
Bio.PDB.FragmentMapper docstring test ... ok
Bio.PDB.HSExposure docstring test ... ok
Bio.PDB.MMCIF2Dict docstring test ... ok
Bio.PDB.MMCIFParser docstring test ... ok
Bio.PDB.Model docstring test ... ok
Bio.PDB.NACCESS docstring test ... ok
Bio.PDB.NeighborSearch docstring test ... ok
Bio.PDB.PDBExceptions docstring test ... ok
Bio.PDB.PDBIO docstring test ... ok
Bio.PDB.PDBList docstring test ... ok
Bio.PDB.PDBParser docstring test ... ok
Bio.PDB.PICIO docstring test ... ok
Bio.PDB.PSEA docstring test ... ok
Bio.PDB.Polypeptide docstring test ... ok
Bio.PDB.QCPSuperimposer docstring test ... ok
Bio.PDB.QCPSuperimposer.qcprotmodule docstring test ... ok
Bio.PDB.Residue docstring test ... ok
Bio.PDB.ResidueDepth docstring test ... ok
Bio.PDB.SASA docstring test ... ok
Bio.PDB.SCADIO docstring test ... ok
Bio.PDB.Selection docstring test ... ok
Bio.PDB.Structure docstring test ... ok
Bio.PDB.StructureAlignment docstring test ... ok
Bio.PDB.StructureBuilder docstring test ... ok
Bio.PDB.Superimposer docstring test ... ok
Bio.PDB.ccealign docstring test ... ok
Bio.PDB.cealign docstring test ... ok
Bio.PDB.ic_data docstring test ... ok
Bio.PDB.ic_rebuild docstring test ... ok
Bio.PDB.internal_coords docstring test ... ok
Bio.PDB.kdtrees docstring test ... ok
Bio.PDB.mmcifio docstring test ... ok
Bio.PDB.mmtf docstring test ... ok
Bio.PDB.mmtf.DefaultParser docstring test ... ok
Bio.PDB.mmtf.mmtfio docstring test ... ok
Bio.PDB.parse_pdb_header docstring test ... ok
Bio.PDB.qcprot docstring test ... ok
Bio.PDB.vectors docstring test ... ok
Bio.Pathway docstring test ... ok
Bio.Pathway.Rep docstring test ... ok
Bio.Pathway.Rep.Graph docstring test ... ok
Bio.Pathway.Rep.MultiGraph docstring test ... ok
Bio.Phylo docstring test ... ok
Bio.Phylo.Applications docstring test ... ok
Bio.Phylo.Applications._Fasttree docstring test ... ok
Bio.Phylo.Applications._Phyml docstring test ... ok
Bio.Phylo.Applications._Raxml docstring test ... ok
Bio.Phylo.BaseTree docstring test ... ok
Bio.Phylo.CDAO docstring test ... ok
Bio.Phylo.CDAOIO docstring test ... ok
Bio.Phylo.Consensus docstring test ... ok
Bio.Phylo.NeXML docstring test ... ok
Bio.Phylo.NeXMLIO docstring test ... ok
Bio.Phylo.Newick docstring test ... ok
Bio.Phylo.NewickIO docstring test ... ok
Bio.Phylo.NexusIO docstring test ... ok
Bio.Phylo.PAML docstring test ... ok
Bio.Phylo.PAML._paml docstring test ... ok
Bio.Phylo.PAML._parse_baseml docstring test ... ok
Bio.Phylo.PAML._parse_codeml docstring test ... ok
Bio.Phylo.PAML._parse_yn00 docstring test ... ok
Bio.Phylo.PAML.baseml docstring test ... ok
Bio.Phylo.PAML.chi2 docstring test ... ok
Bio.Phylo.PAML.codeml docstring test ... ok
Bio.Phylo.PAML.yn00 docstring test ... ok
Bio.Phylo.PhyloXML docstring test ... ok
Bio.Phylo.PhyloXMLIO docstring test ... ok
Bio.Phylo.TreeConstruction docstring test ... ok
Bio.Phylo._cdao_owl docstring test ... ok
Bio.Phylo._io docstring test ... ok
Bio.Phylo._utils docstring test ... ok
Bio.PopGen docstring test ... ok
Bio.PopGen.GenePop docstring test ... ok
Bio.PopGen.GenePop.Controller docstring test ... ok
Bio.PopGen.GenePop.EasyController docstring test ... ok
Bio.PopGen.GenePop.FileParser docstring test ... ok
Bio.PopGen.GenePop.LargeFileParser docstring test ... ok
Bio.Restriction docstring test ... ok
Bio.Restriction.PrintFormat docstring test ... ok
Bio.Restriction.Restriction docstring test ... ok
Bio.Restriction.Restriction_Dictionary docstring test ... ok
Bio.SCOP docstring test ... ok
Bio.SCOP.Cla docstring test ... ok
Bio.SCOP.Des docstring test ... ok
Bio.SCOP.Dom docstring test ... ok
Bio.SCOP.Hie docstring test ... ok
Bio.SCOP.Raf docstring test ... ok
Bio.SCOP.Residues docstring test ... ok
Bio.SVDSuperimposer docstring test ... ok
Bio.SearchIO docstring test ... ok
Bio.SearchIO.BlastIO docstring test ... ok
Bio.SearchIO.BlastIO.blast_tab docstring test ... ok
Bio.SearchIO.BlastIO.blast_text docstring test ... ok
Bio.SearchIO.BlastIO.blast_xml docstring test ... ok
Bio.SearchIO.BlatIO docstring test ... ok
Bio.SearchIO.ExonerateIO docstring test ... ok
Bio.SearchIO.ExonerateIO._base docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... ok
Bio.SearchIO.FastaIO docstring test ... ok
Bio.SearchIO.HHsuiteIO docstring test ... ok
Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... ok
Bio.SearchIO.HmmerIO docstring test ... ok
Bio.SearchIO.HmmerIO._base docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... ok
Bio.SearchIO.InterproscanIO docstring test ... ok
Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... ok
Bio.SearchIO._index docstring test ... ok
Bio.SearchIO._legacy docstring test ... ok
Bio.SearchIO._legacy.NCBIStandalone docstring test ... ok
Bio.SearchIO._legacy.ParserSupport docstring test ... ok
Bio.SearchIO._model docstring test ... ok
Bio.SearchIO._model._base docstring test ... ok
Bio.SearchIO._model.hit docstring test ... ok
Bio.SearchIO._model.hsp docstring test ... ok
Bio.SearchIO._model.query docstring test ... ok
Bio.SearchIO._utils docstring test ... ok
Bio.Seq docstring test ... ok
Bio.SeqFeature docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.AbiIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqIO.FastaIO docstring test ... ok
Bio.SeqIO.GckIO docstring test ... ok
Bio.SeqIO.IgIO docstring test ... ok
Bio.SeqIO.InsdcIO docstring test ... ok
Bio.SeqIO.Interfaces docstring test ... ok
Bio.SeqIO.NibIO docstring test ... ok
Bio.SeqIO.PdbIO docstring test ... ok
Bio.SeqIO.PhdIO docstring test ... ok
Bio.SeqIO.PirIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.SeqXmlIO docstring test ... ok
Bio.SeqIO.SffIO docstring test ... ok
Bio.SeqIO.SnapGeneIO docstring test ... ok
Bio.SeqIO.SwissIO docstring test ... ok
Bio.SeqIO.TabIO docstring test ... ok
Bio.SeqIO.TwoBitIO docstring test ... ok
Bio.SeqIO.UniprotIO docstring test ... ok
Bio.SeqIO.XdnaIO docstring test ... ok
Bio.SeqIO._index docstring test ... ok
Bio.SeqIO._twoBitIO docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.SeqUtils.CheckSum docstring test ... ok
Bio.SeqUtils.CodonUsage docstring test ... ok
Bio.SeqUtils.CodonUsageIndices docstring test ... ok
Bio.SeqUtils.IsoelectricPoint docstring test ... ok
Bio.SeqUtils.MeltingTemp docstring test ... ok
Bio.SeqUtils.ProtParam docstring test ... ok
Bio.SeqUtils.ProtParamData docstring test ... ok
Bio.SeqUtils.lcc docstring test ... ok
Bio.Sequencing docstring test ... ok
Bio.Sequencing.Ace docstring test ... ok
Bio.Sequencing.Applications docstring test ... ok
Bio.Sequencing.Applications._Novoalign docstring test ... ok
Bio.Sequencing.Applications._bwa docstring test ... ok
Bio.Sequencing.Applications._samtools docstring test ... ok
Bio.Sequencing.Phd docstring test ... ok
Bio.SwissProt docstring test ... ok
Bio.SwissProt.KeyWList docstring test ... ok
Bio.UniGene docstring test ... ok
Bio.UniProt docstring test ... ok
Bio.UniProt.GOA docstring test ... ok
Bio.Wise docstring test ... ok
Bio.Wise.dnal docstring test ... ok
Bio.Wise.psw docstring test ... ok
Bio._utils docstring test ... ok
Bio.bgzf docstring test ... ok
Bio.codonalign docstring test ... ok
Bio.codonalign.codonalignment docstring test ... ok
Bio.codonalign.codonseq docstring test ... ok
Bio.cpairwise2 docstring test ... ok
Bio.kNN docstring test ... ok
Bio.motifs docstring test ... ok
Bio.motifs._pwm docstring test ... ok
Bio.motifs.alignace docstring test ... ok
Bio.motifs.applications docstring test ... ok
Bio.motifs.applications._xxmotif docstring test ... ok
Bio.motifs.clusterbuster docstring test ... ok
Bio.motifs.jaspar docstring test ... ok
Bio.motifs.jaspar.db docstring test ... ok
Bio.motifs.mast docstring test ... ok
Bio.motifs.matrix docstring test ... ok
Bio.motifs.meme docstring test ... ok
Bio.motifs.minimal docstring test ... ok
Bio.motifs.pfm docstring test ... ok
Bio.motifs.thresholds docstring test ... ok
Bio.motifs.transfac docstring test ... ok
Bio.motifs.xms docstring test ... ok
Bio.pairwise2 docstring test ... ok
Bio.phenotype docstring test ... ok
Bio.phenotype.phen_micro docstring test ... ok
Bio.phenotype.pm_fitting docstring test ... ok
BioSQL docstring test ... ok
BioSQL.BioSeq docstring test ... ok
BioSQL.BioSeqDatabase docstring test ... ok
BioSQL.DBUtils docstring test ... ok
BioSQL.Loader docstring test ... ok
----------------------------------------------------------------------
Ran 551 tests in 441.832 seconds

Skipping any tests requiring internet access
Python version: 3.11.6 (main, Oct  8 2023, 05:06:43) [GCC 12.2.0]
Operating system: posix linux
	rm -fr -- /tmp/dh-xdg-rundir-vtW1Zejf
mv Tests_avoid/* Tests
rmdir Tests_avoid
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -a -O--buildsystem=pybuild
   dh_prep -a -O--buildsystem=pybuild
	rm -f -- debian/python3-biopython.substvars
	rm -fr -- debian/.debhelper/generated/python3-biopython/ debian/python3-biopython/ debian/tmp/
	rm -f debian/python3-biopython.debhelper.log
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
	install -m0755 -d /<<BUILDDIR>>/python-biopython-1.81\+dfsg/debian/tmp
	pybuild --install -i python{version} -p 3.11 --dest-dir /<<BUILDDIR>>/python-biopython-1.81\+dfsg/debian/tmp
I: pybuild base:310: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/tmp 
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running build
running build_py
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are
        already explicitly excluding 'Bio.Align.substitution_matrices.data' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'Bio.Entrez.DTDs' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'Bio.Entrez.DTDs' to be distributed and are
        already explicitly excluding 'Bio.Entrez.DTDs' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'Bio.Entrez.XSDs' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'Bio.Entrez.XSDs' to be distributed and are
        already explicitly excluding 'Bio.Entrez.XSDs' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
running build_ext
running install_lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/File.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/LogisticRegression.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/MarkovModel.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/MaxEntropy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NaiveBayes.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Seq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqFeature.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqRecord.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/_utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/bgzf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/kNN.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/pairwise2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Affy/CelFile.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Affy/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Affy/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Affy/__pycache__/CelFile.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/AlignInfo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/a2m.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/bed.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/bigbed.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/bigmaf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/bigpsl.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/clustal.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/emboss.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/exonerate.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/fasta.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/hhr.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/interfaces.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/maf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/mauve.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/msf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/nexus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/phylip.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/psl.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/sam.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/stockholm.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/tabular.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_ClustalOmega.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Clustalw.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Dialign.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_MSAProbs.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Mafft.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Prank.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Probcons.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_TCoffee.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Muscle.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_Muscle.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_Clustalw.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_ClustalOmega.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_Prank.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_Mafft.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_Dialign.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_Probcons.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_TCoffee.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/__pycache__/_MSAProbs.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BENNER22 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BENNER6 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BENNER74 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLASTN -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLASTP -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM45 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM50 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM62 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM80 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/BLOSUM90 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/DAYHOFF -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/FENG -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/GENETIC -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/GONNET1992 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/HOXD70 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/JOHNSON -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/JONES -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/LEVIN -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/MCLACHLAN -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/MDM78 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/MEGABLAST -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/NUC.4.4 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/PAM250 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/PAM30 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/PAM70 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/RAO -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/RISLER -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/SCHNEIDER -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/STR -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data/TRANS -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/data
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/_aligners.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/AlignInfo.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/a2m.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/interfaces.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/bed.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/bigbed.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/bigmaf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/maf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/bigpsl.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/clustal.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/emboss.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/exonerate.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/fasta.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/hhr.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/mauve.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/msf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/nexus.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/phylip.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/psl.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/sam.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/stockholm.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/__pycache__/tabular.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/ClustalIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/EmbossIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/Interfaces.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/MafIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/MauveIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/MsfIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/NexusIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/PhylipIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/StockholmIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/ClustalIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/Interfaces.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/EmbossIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/FastaIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/MafIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/MauveIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/MsfIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/NexusIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/PhylipIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/AlignIO/__pycache__/StockholmIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Alphabet
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Alphabet/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Alphabet
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Application
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Application/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Application
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Application/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Application/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Application/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/Applications.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/NCBIWWW.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/NCBIXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/ParseBlastTable.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/Record.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/__pycache__/Record.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/__pycache__/NCBIXML.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/__pycache__/Applications.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/__pycache__/NCBIWWW.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Blast/__pycache__/ParseBlastTable.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/CAPS
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/CAPS/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/CAPS
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/CAPS/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/CAPS/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/CAPS/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster/cluster.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster/cluster.h -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster/clustermodule.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Cluster/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/codonalignment.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/codonseq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/__pycache__/codonseq.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/__pycache__/codonalignment.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Compass
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Compass/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Compass
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Compass/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Compass/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Compass/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/CodonTable.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/IUPACData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/PDBData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/SCOPData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/__pycache__/CodonTable.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/__pycache__/IUPACData.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/__pycache__/PDBData.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Data/__pycache__/SCOPData.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss/Applications.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss/Primer3.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss/PrimerSearch.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss/__pycache__/Applications.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss/__pycache__/PrimerSearch.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Emboss/__pycache__/Primer3.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/Parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/EMBL_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/GenBank_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/HomoloGene.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-common1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-display1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-format1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-link1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-list1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-math1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-para1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-references1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-section1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Features.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Access.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Project.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NCBI_all.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NSE.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/NSE.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/OMSSA.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PDB_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PIR_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PRF_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/SP_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/SP_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivearticle.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivecustom-classes.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivecustom-models.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/archivecustom-modules.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/articlemeta.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/backmatter.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/chars.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/common.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/default-classes.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/default-mixes.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/display.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eInfo_020511.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eLink_090910.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eLink_101123.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/ePost_020511.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eSearch_020511.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eSpell.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/eSummary_041029.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/egquery.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/einfo.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/elink.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/elink_020122.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/epost.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/esearch.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/esummary-v1.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/esummary_gene.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/format.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/htmltable.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsa.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsb.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsc.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsn.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamso.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isoamsr.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isobox.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isocyr1.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isocyr2.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isodia.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isogrk1.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isogrk2.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isogrk3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isogrk4.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isolat1.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isolat2.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isomfrk.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isomopf.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isomscr.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isonum.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isopub.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/isotech.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/journalmeta.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/link.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/list.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/math.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathml2.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathml3-qname1.mod -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathml3.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mathmlsetup.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mmlalias.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/mmlextra.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/modules.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/notat.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/para.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/phrase.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pmc-1.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_020114.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_100101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_100301.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_110101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_120101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_130101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_130501.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_140101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_150101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_180101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_180601.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/pubmed_190101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/references.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/section.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/taxon.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/xhtml-table-1.mod -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs/xmlspecchars.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/DTDs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/XSDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs/IPGReportSet.xsd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/XSDs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/__pycache__/Parser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/Enzyme.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/Prodoc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/Prosite.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/ScanProsite.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/cellosaurus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/__pycache__/Enzyme.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/__pycache__/Prodoc.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/__pycache__/Prosite.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/__pycache__/cellosaurus.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/ExPASy/__pycache__/ScanProsite.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/Record.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/Scanner.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/__pycache__/utils.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/__pycache__/Scanner.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/GenBank/__pycache__/Record.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Geo/Record.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Geo/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Geo/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Geo/__pycache__/Record.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/BasicChromosome.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/ColorSpiral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/Comparative.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/DisplayRepresentation.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/Distribution.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/KGML_vis.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Colors.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Diagram.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Feature.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Graph.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/_Track.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_Diagram.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_LinearDrawer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_AbstractDrawer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_FeatureSet.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_Feature.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_Colors.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_GraphSet.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_Graph.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_CircularDrawer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_Track.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram/__pycache__/_CrossLink.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/__pycache__/ColorSpiral.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/__pycache__/BasicChromosome.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/__pycache__/DisplayRepresentation.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/__pycache__/Distribution.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/__pycache__/Comparative.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Graphics/__pycache__/KGML_vis.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/DynamicProgramming.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/MarkovModel.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/Trainer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/Utilities.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/__pycache__/MarkovModel.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/__pycache__/Trainer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/__pycache__/DynamicProgramming.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/HMM/__pycache__/Utilities.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/REST.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Compound
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Compound
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Compound/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Compound/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Enzyme
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Enzyme
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Enzyme/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Enzyme/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Gene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Gene
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Gene/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Gene/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Map
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Map
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Map/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/Map/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Map/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/KGML_parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/KGML_pathway.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/__pycache__/KGML_parser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML/__pycache__/KGML_pathway.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/KEGG/__pycache__/REST.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/DefaultParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/mmtfio.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/__pycache__/DefaultParser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf/__pycache__/mmtfio.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/AbstractPropertyMap.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Atom.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Chain.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/DSSP.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Dice.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Entity.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/FragmentMapper.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/HSExposure.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/MMCIF2Dict.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/MMCIFParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Model.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/NACCESS.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/NeighborSearch.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/PDBExceptions.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/PDBIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/PDBList.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/PDBParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/PICIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/PSEA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Polypeptide.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Residue.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/ResidueDepth.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/SASA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/SCADIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Selection.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Structure.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/StructureAlignment.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/StructureBuilder.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Superimposer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/cealign.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/ic_data.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/ic_rebuild.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/internal_coords.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/mmcifio.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/parse_pdb_header.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/qcprot.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/vectors.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/ccealignmodule.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/kdtrees.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/PDBParser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/PDBExceptions.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/StructureBuilder.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Structure.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Entity.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Model.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/internal_coords.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Atom.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/vectors.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/ic_data.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Chain.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Residue.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/parse_pdb_header.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/MMCIFParser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/MMCIF2Dict.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/PDBList.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Polypeptide.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/PDBIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/mmcifio.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Selection.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Superimposer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/cealign.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/qcprot.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/StructureAlignment.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/DSSP.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/AbstractPropertyMap.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/ResidueDepth.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/HSExposure.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/FragmentMapper.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/Dice.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/NeighborSearch.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/SASA.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/NACCESS.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/PSEA.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/ic_rebuild.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/PICIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/__pycache__/SCADIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Medline
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Medline/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Medline
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Medline/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Medline/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Medline/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/alignace.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/clusterbuster.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/mast.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/matrix.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/meme.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/minimal.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/pfm.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/thresholds.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/transfac.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/xms.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/applications/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/applications/_xxmotif.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/applications/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/applications/__pycache__/_xxmotif.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar/db.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar/__pycache__/db.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/_pwm.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/matrix.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/meme.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/transfac.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/thresholds.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/alignace.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/clusterbuster.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/pfm.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/xms.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/mast.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/motifs/__pycache__/minimal.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/Nexus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/Nodes.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/StandardData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/Trees.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/cnexus.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/__pycache__/Nexus.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/__pycache__/StandardData.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/__pycache__/Trees.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Nexus/__pycache__/Nodes.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR/NOEtools.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR/xpktools.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR/__pycache__/xpktools.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/NMR/__pycache__/NOEtools.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/Graph.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/MultiGraph.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/__pycache__/MultiGraph.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep/__pycache__/Graph.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Pathway/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype/phen_micro.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype/pm_fitting.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype/__pycache__/phen_micro.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/phenotype/__pycache__/pm_fitting.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/Controller.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/EasyController.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/FileParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/LargeFileParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/__pycache__/FileParser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/__pycache__/Controller.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/__pycache__/EasyController.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop/__pycache__/LargeFileParser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PopGen/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction/PrintFormat.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction/Restriction.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction/Restriction_Dictionary.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction/__pycache__/Restriction.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction/__pycache__/Restriction_Dictionary.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Restriction/__pycache__/PrintFormat.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/Cla.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/Des.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/Dom.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/Hie.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/Raf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/Residues.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/__pycache__/Des.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/__pycache__/Cla.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/__pycache__/Residues.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/__pycache__/Hie.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/__pycache__/Dom.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SCOP/__pycache__/Raf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlatIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/NCBIStandalone.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/ParserSupport.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/__pycache__/NCBIStandalone.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy/__pycache__/ParserSupport.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/_base.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/hit.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/hsp.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/query.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/__pycache__/query.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/__pycache__/_base.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/__pycache__/hit.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model/__pycache__/hsp.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/blast_tab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/blast_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/blast_xml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/__pycache__/blast_tab.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/__pycache__/blast_xml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO/__pycache__/blast_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO/__pycache__/hhsuite2_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/_base.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/__pycache__/hmmer2_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/__pycache__/_base.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/__pycache__/hmmer3_domtab.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/__pycache__/hmmer3_tab.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO/__pycache__/hmmer3_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/_base.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/__pycache__/exonerate_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/__pycache__/_base.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/__pycache__/exonerate_vulgar.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO/__pycache__/exonerate_cigar.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO/__pycache__/interproscan_xml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/__pycache__/_utils.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/__pycache__/_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/__pycache__/BlatIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SearchIO/__pycache__/FastaIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/AbiIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/AceIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/GckIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/IgIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/NibIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/PdbIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/PhdIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/PirIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/QualityIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SffIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SnapGeneIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SwissIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/TabIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/TwoBitIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/UniprotIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/XdnaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_twoBitIO.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/AbiIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/Interfaces.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/AceIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/FastaIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/GckIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/IgIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/InsdcIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/NibIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/PdbIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/PhdIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/QualityIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/PirIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/SeqXmlIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/SffIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/SnapGeneIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/SwissIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/TabIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/TwoBitIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/UniprotIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/XdnaIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/__pycache__/_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/CheckSum.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/CodonUsage.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/CodonUsageIndices.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/IsoelectricPoint.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/MeltingTemp.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/ProtParam.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/ProtParamData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/lcc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/CheckSum.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/ProtParam.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/ProtParamData.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/IsoelectricPoint.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/lcc.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/CodonUsage.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/CodonUsageIndices.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqUtils/__pycache__/MeltingTemp.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Ace.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Phd.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/_Novoalign.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/_bwa.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/_samtools.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/__pycache__/_Novoalign.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/__pycache__/_bwa.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications/__pycache__/_samtools.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/__pycache__/Ace.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Sequencing/__pycache__/Phd.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SVDSuperimposer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SVDSuperimposer
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SVDSuperimposer/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SVDSuperimposer/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SwissProt/KeyWList.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SwissProt/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SwissProt/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SwissProt/__pycache__/KeyWList.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/TogoWS
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/TogoWS/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/TogoWS
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/TogoWS/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/TogoWS/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/TogoWS/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/BaseTree.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/CDAO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/CDAOIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Consensus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/NeXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/NeXMLIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Newick.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/NewickIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/NexusIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PhyloXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PhyloXMLIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/TreeConstruction.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/_cdao_owl.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/_io.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/_utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/_Fasttree.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/_Phyml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/_Raxml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/__pycache__/_Phyml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/__pycache__/_Raxml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications/__pycache__/_Fasttree.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/_paml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/_parse_baseml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/_parse_codeml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/_parse_yn00.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/baseml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/chi2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/codeml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/yn00.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/chi2.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/baseml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/_paml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/_parse_baseml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/codeml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/_parse_codeml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/yn00.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML/__pycache__/_parse_yn00.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/_io.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/BaseTree.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/NewickIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/Newick.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/NexusIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/PhyloXMLIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/PhyloXML.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/NeXMLIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/NeXML.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/_cdao_owl.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/CDAOIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/CDAO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/_utils.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/TreeConstruction.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Phylo/__pycache__/Consensus.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniGene/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniGene
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniGene/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniGene/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniGene/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniProt/GOA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniProt/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniProt/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/UniProt/__pycache__/GOA.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise/dnal.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise/psw.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise/__pycache__/psw.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Wise/__pycache__/dnal.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/cpairwise2module.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/Seq.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/SeqRecord.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/File.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/SeqFeature.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/bgzf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/LogisticRegression.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/MarkovModel.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/NaiveBayes.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/pairwise2.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/kNN.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/MaxEntropy.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/__pycache__/_utils.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/BioSeq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/BioSeqDatabase.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/DBUtils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/Loader.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/__pycache__/BioSeq.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/__pycache__/BioSeqDatabase.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/__pycache__/Loader.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/BioSQL/__pycache__/DBUtils.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.config
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.config/biopython
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.config/biopython/Bio
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.config/biopython/Bio/Entrez
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.config/biopython/Bio/Entrez/DTDs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.config/biopython/Bio/Entrez/XSDs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.config/matplotlib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.cache
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.cache/matplotlib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home/.cache/matplotlib/fontlist-v330.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.cache/matplotlib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.t_coffee
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.t_coffee/cache
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.t_coffee/mcoffee
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.t_coffee/methods
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.t_coffee/plugins
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/home/.t_coffee/plugins/linux
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/ACT_example.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/PF05371_seed.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/Plates.csv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/Proux_et_al_2002_Figure_6.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/alpha.faa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/beta.faa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/clustal_run.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/ec_5.4.2.2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/fasta_dictionary.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/fasta_iterator.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/ls_orchid.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/ls_orchid.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/ls_orchid.gbk.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/ls_orchid.gbk.bz2 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/ls_orchid.gbk.gz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/m_cold.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/my_blast.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/my_blat.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/nmr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/nmr/noed.xpk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/nmr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/nmr/simplepredict.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/nmr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/opuntia.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/opuntia.dnd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/opuntia.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/simple.dnd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/swissprot.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples/www_blast.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_appendix.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_blast.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_cluster.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_contributing.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_cookbook.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_entrez.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_graphics.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_introduction.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_kegg.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_learning.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_motifs.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_pdb.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_phenotype.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_phylo.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_popgen.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_quick_start.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_searchio.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_seq_annot.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_seq_objects.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_seqio.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_testing.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_uniprot.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_align.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_introduction.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_quick_start.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_seq_objects.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_seq_annot.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_seqio.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_align.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_blast.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_searchio.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_entrez.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_uniprot.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_pdb.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_popgen.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_phylo.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_motifs.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_cluster.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_learning.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_graphics.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_kegg.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_phenotype.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_cookbook.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_testing.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_contributing.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/Tutorial/chapter_appendix.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/Tutorial
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/.coveragerc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/310.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/3100.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/3730.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/A6_1-DB3.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/empty.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/fake.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/no_smpl1.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/nonascii_encoding.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/test.fsa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Abi/test_data -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Abi
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Ace
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Ace/consed_sample.ace -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Ace
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Ace/contig1.ace -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Ace
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Ace/seq.cap.ace -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Ace
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Affy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Affy/affy_v3_example.CEL -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Affy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Affy/affy_v4_example.CEL -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Affy
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/bsubtilis.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/bsubtilis.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/cow.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/cow.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/ecoli.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/ecoli.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/hg38.chrom.sizes -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/pig.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Align/pig.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Align
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BWA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/BWA/HNSCC1_1_truncated.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BWA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/BWA/HNSCC1_2_truncated.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BWA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/BWA/human_g1k_v37_truncated.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BWA
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/BioSQL/biosqldb-mysql.sql -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/BioSQL/biosqldb-pg.sql -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/BioSQL/biosqldb-sqlite.sql -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/BioSQL/cor6_6.db -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/BioSQL
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mirna.tab -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mirna.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mock_actin.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mock_disco.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mock_orchid.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mock_pcr.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mock_short_empty.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mock_short_result.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/mock_wait.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_005.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_006.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_007.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_008.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_009.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_010.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_011.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_012.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2226_tblastn_013.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2228_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/tab_2228_tblastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastp_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastp_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastp_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastp_005.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastp_006.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastp_007.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_blastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_phiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_phiblast_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_phiblast_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_tblastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2010L_tblastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastp_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastp_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastp_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastp_005.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastp_006.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastp_007.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_blastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_phiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_phiblast_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_phiblast_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_tblastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2011L_tblastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2012L_psiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2014L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2014L_psiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2102L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2201L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2202L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2202L_blastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2202L_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2208L_psiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2215L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2216L_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2220L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2220L_blastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2221L_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2222L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2222_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastp_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastp_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastp_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastx_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_blastx_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_tblastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_tblastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_tblastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_tblastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_tblastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_tblastx_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2226_tblastx_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/text_2230_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/wnts.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/wnts.xml.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2212L_blastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2212L_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2212L_blastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2212L_tblastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2212L_tblastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2218L_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2218L_rpsblast_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2218_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2218_blastp_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2222_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2222_blastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastn_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastn_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastn_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastn_005.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastn_006.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastp_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastp_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastp_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastp_005.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastx_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastx_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_blastx_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastn_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastn_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastn_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastn_005.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastx_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastx_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2226_tblastx_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_blastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_blastn_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_blastp_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_blastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_blastx_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_tblastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_tblastn_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_tblastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/xml_2900_tblastx_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blast/html_msgid_29_blastx_001.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blast
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/CAG33136.1.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/balAcu1.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed12.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed12.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed3.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed3.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed4.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed4.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed5.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed5.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed6.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed6.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed7.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed7.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed8.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed8.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed9.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bed9.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bigPsl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bigbed_extended.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bigbedtest.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/bigbedtest.psl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/dna.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/dna_rna.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/dna_rna.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/dna_rna.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/dna_rna.psl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/dna_rna.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/fasta_34.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/hg38.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/mirna.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_001.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_001.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_001.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_001.psl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_001.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_002.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_003.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_003.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_003.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_003.psl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_003.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_004.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_004.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_004.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_004.psl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_004.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_005.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_005.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_005.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_005.psl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_34_005.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_35_001.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_35_001.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_35_001.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_35_001.psl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_35_002.bed -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_35_002.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/psl_35_002.psl.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/pslx_34_001.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/pslx_34_002.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/pslx_34_003.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/pslx_34_004.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/pslx_34_005.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/pslx_35_001.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/pslx_35_002.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Blat/rna.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Blat
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/CDAO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/CDAO/test.cdao -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/CDAO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Cellosaurus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Cellosaurus/cell_lines_1.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Cellosaurus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Cellosaurus/cell_lines_2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Cellosaurus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Cellosaurus/cell_lines_3.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Cellosaurus
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/clustalw.a2m -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/clustalw.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/clustalw.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/hedgehog.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/kalign.a2m -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/kalign.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/kalign.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/msaprobs.a2m -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/msaprobs.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/msaprobs.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/muscle.a2m -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/muscle.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/muscle.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/odd_consensus.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/opuntia.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/probcons.a2m -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/probcons.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/probcons.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/promals3d.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/protein.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Clustalw/temp horses.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Clustalw
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Cluster/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Cluster/cyano.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Cluster
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/CodonUsage
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/CodonUsage/HighlyExpressedGenes.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/CodonUsage
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Compass
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Compass/comtest1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Compass
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Compass/comtest2 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Compass
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/101ma_no_coords.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/A04195.imgt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/AAA03323.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/AE017046.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/DD231055_edited.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/DD231055_edited2.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/DS830848.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/Human_contigs.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/RepBase23.02.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/SC10H5.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/TRBG361.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/U87107.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/embl_with_0_line.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/epo_prt_selection.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/hla_3260_sample.imgt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/kipo_prt_sample.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/location_wrap.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/patents.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/EMBL/xx_after_co.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/EMBL
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/NirK.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/NirK_full.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/alignret.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/bac_find.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/bac_find.psearch -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/cds_forward.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/cds_reverse.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/emboss_pair_aln_full_blank_line.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/internal_oligo.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/matcher_pair.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/matcher_simple.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/needle.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/needle_asis.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/needle_nobrief_multiple.pair -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/needle_overhang.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/no_oligo.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/short.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/water.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/water2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/water_reverse1.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/water_reverse2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/water_reverse3.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Emboss/water_reverse4.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Emboss
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/biosample.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/efetch_pmc.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/efetch_schemas.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/egquery1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/egquery2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/einfo1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/einfo2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/einfo3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/einfo4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/elink1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/elink2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/elink3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/elink4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/elink5.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/elink6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/elink7.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/elink8.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/epost1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/epost2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/epost3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esearch1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esearch2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esearch3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esearch4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esearch5.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esearch6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esearch7.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esearch8.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/espell.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary5.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary7.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary8.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/esummary9.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/journals.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/ncbi_mim.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/nucleotide1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/nucleotide2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/protein.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/pubmed1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/pubmed2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/pubmed3.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/pubmed4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/pubmed5.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/pubmed6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/pubmed7.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Entrez/taxonomy.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Entrez
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Enzymes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Enzymes/lactate.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Enzymes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Enzymes/lipoprotein.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Enzymes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Enzymes/proline.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Enzymes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Enzymes/valine.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Enzymes
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_affine_local.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_affine_local_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_affine_local_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_cdna2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_cdna2genome_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_cdna2genome_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_cigar_fshifts.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_coding2coding.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_coding2coding_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_coding2coding_fshifts.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_coding2coding_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_coding2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_coding2genome_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_coding2genome_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_dna2protein.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_dna2protein_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_dna2protein_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_est2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_est2genome_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_est2genome_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_genome2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ner.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ner_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ner_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_protein2dna.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_protein2dna_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_protein2dna_fshifts.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_protein2dna_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_protein2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_protein2genome_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_protein2genome_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ungapped.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ungapped_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ungapped_trans.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ungapped_trans_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ungapped_trans_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_m_ungapped_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_o_cigar_fshifts2.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_o_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_o_vulgar_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_o_vulgar_fshifts.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_o_vulgar_fshifts2.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_q_multiple.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_q_multiple_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_q_multiple_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_22_q_none.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_24_m_protein2genome_met_intron.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_24_m_protein2genome_met_intron_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_24_m_protein2genome_met_intron_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_24_m_protein2genome_revcomp_fshifts.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_24_m_protein2genome_revcomp_fshifts_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Exonerate/exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Exonerate
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/ExtendedPhylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/ExtendedPhylip/primates.phyx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/ExtendedPhylip
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/FSSP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/FSSP/1cnv.fssp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/FSSP
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/aster.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/aster_no_wrap.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/centaurea.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/dups.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/elderberry.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/f001 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/f002 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/f003 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/fa01 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/flowers.pro.gz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/lavender.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/loveliesbleeding.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/lupine.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/nucleotide_lib.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/nucleotide_m8CB.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/nucleotide_m8CC.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output001.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output002.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output003.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output004.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output005.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output006.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output007.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output008.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output009.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output010.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output011.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output012.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output013.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output014.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output015.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/output016.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/phlox.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/protein_lib.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/protein_m8CB.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/protein_m8CC.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/rose.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/rosemary.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/sweetpea.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/wisteria.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Fasta/tc_out.msf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Fasta
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GFF/NC_001422.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GFF/NC_001802.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GFF/NC_001802lc.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GFF/NC_001802x.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GFF/multi.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GFF
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Gck
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Gck/artificial.gck -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Gck
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/1MRR_A.gp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/DS830848.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/EU851978.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/EU851978_output.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/GU949562.1.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/HM138502.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/HM138502_output.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/KF527485.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/KF527485_output.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NC_000932.faa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NC_000932.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NC_000932.gb.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NC_005816.faa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NC_005816.ffn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NC_005816.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NC_005816.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NC_005816.tsv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NP_416719.gbwithparts -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/NT_019265.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/addgene-plasmid-11664-sequence-180430.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/addgene-plasmid-39296-sequence-49545.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/arab1.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/bad_loc_wrap.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/bad_origin_wrap.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/bad_origin_wrap_CDS.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/bad_origin_wrap_fuzzy.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/bad_origin_wrap_linear.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/blank_seq.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/cor6_6.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/cor6_6.gb.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/dbsource_wrap.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/empty_accession.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/empty_feature_qualifier.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/empty_version.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/extra_keywords.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/gbvrl1_start.seq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/invalid_locus_line_spacing.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/invalid_misc_feature.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/invalid_product.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/invalid_structured_comment.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/iro.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/negative_location.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/no_end_marker.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/no_origin_no_end.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/noref.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/one_of.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/origin_line.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/pBAD30.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/pri1.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/protein_refseq.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/protein_refseq2.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/qualifier_escaping_read.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/qualifier_escaping_write.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/tls_KDHP01000000.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/tsa_acropora.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/GenBank/wrong_sequence_indent.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/GenBank
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/GSE16.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/GSM645.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/GSM691.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/GSM700.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/GSM804.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/soft_ex_affy.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/soft_ex_affy_chp.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/soft_ex_dual.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/soft_ex_family.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/soft_ex_platform.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Geo/soft_ex_series.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Geo
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/spiral_test.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/square_test.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_by_meth_linear.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_by_meth_circular.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_by_obj_circular.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_by_obj_frag_circular.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_by_obj_linear.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_by_obj_frag_linear.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_region_linear.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_region_linear.svg -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_region_circular.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_region_circular.svg -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/line_graph.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/line_graph_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/labels_default.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/labels_default.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/labels_default_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigils.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigils.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigils_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_arrows.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_arrows.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_arrows_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_arrow_shafts.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_arrow_shafts.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_arrow_shafts_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_bigarrow_shafts.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_bigarrow_shafts.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_bigarrow_shafts_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_labels.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_labels.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_labels_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_ARROW.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_ARROW.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_ARROW_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_BIGARROW.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_BIGARROW.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_BIGARROW_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_JAGGY.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_JAGGY.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_JAGGY_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_OCTO.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_OCTO.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_long_OCTO_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_ARROW.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_ARROW.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_ARROW_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_BIGARROW.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_BIGARROW.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_BIGARROW_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_JAGGY.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_JAGGY.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_JAGGY_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_OCTO.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_OCTO.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/GD_sigil_short_OCTO_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/random_organism.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/organism.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/organism.eps -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/organism.svg -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/tRNA_chrom_sf.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/tRNA_chrom.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/multi_bar.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/simple_bar.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/scatter_test_1.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/scatter_test_7.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/map01100_original.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/map03070_original.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/map01100_widths.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/map03070_colors.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/map01100_transparency.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Graphics/map03070_transparency.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Graphics
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/2uvo_hhblits.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/2uvo_hhblits_emptytable.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/2uvo_hhblits_onlyheader.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/2uvo_hhsearch.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/4p79_hhsearch_server_NOssm.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/4y9h_hhsearch_server_NOssm.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/allx.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/hhpred_9590198.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/HHsuite/hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/HHsuite
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/domtab_30_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/domtab_30_hmmscan_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/domtab_30_hmmscan_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/domtab_30_hmmscan_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/domtab_30_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/domtab_31b1_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/domtab_31b1_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/tab_30_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/tab_30_hmmscan_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/tab_30_hmmscan_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/tab_30_hmmscan_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/tab_31b1_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/tab_31b1_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_20_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_21_hmmpfam_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_22_hmmpfam_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_22_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_23_hmmpfam_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_23_hmmpfam_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_23_hmmpfam_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_23_hmmpfam_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_24_hmmpfam_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_005.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_006.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_007.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_008.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_009.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmscan_010.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmsearch_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmsearch_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmsearch_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_30_hmmsearch_005.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_31b1_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_31b1_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_31b2_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_31b2_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_31b2_hmmsearch_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Hmmer/text_31b2_phmmer_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Hmmer
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/IntelliGenetics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/IntelliGenetics/TAT_mase_nuc.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/IntelliGenetics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/IntelliGenetics/VIF_mase-pro.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/IntelliGenetics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/IntelliGenetics/vpu_nucaligned.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/IntelliGenetics
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/InterProScan
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/InterProScan/test_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/InterProScan
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/compound.irregular -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/compound.sample -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/enzyme.4letter -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/enzyme.irregular -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/enzyme.new -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/enzyme.sample -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/gene.sample -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/ko00010.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/ko00253.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/ko01100.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/ko03070.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/map00950.rea -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/map01100.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/KEGG/map03070.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/KEGG
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/bug2453.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/bundle_without_target.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/bundle_without_target.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/cnksr3.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/corrupt.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/humor.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/invalid.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/length_coords_mismatch.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_mm9_chr10.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_mm9_chr10.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_mm9_chr10.mafindex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_mm9_chr10_bad.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_mm9_chr10_bad.mafindex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_mm9_chr10_big.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_mm9_chr10_big.mafindex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_test.bb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/ucsc_test.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/unfinished.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MAF/wrong_version.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MAF
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/canFam2.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/combined.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/combined.xmfa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/combined.xmfa.backbone -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/combined.xmfa.bbcols -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/equCab1.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/mm9.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/separate.xmfa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/separate.xmfa.backbone -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/separate.xmfa.bbcols -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/simple.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/simple.xmfa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/simple.xmfa.backbone -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/simple.xmfa.bbcols -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Mauve/simple_short.xmfa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Mauve
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Medline
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Medline/pubmed_result1.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Medline
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Medline/pubmed_result2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Medline
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Medline/pubmed_result3.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Medline
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MetaTool/Meta3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MetaTool/Meta4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MetaTool/Meta6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MetaTool/Meta7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MetaTool/Meta8.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MetaTool/meta.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MetaTool/meta2.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/MetaTool/meta9.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/MetaTool
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NBRF/B_nuc.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NBRF/Cw_prot.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NBRF/DMA_nuc.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NBRF/DMB_prot.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NBRF/clustalw.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NBRF
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NMR/noed.xpk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NMR/out_example.xpk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NMR
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/characters.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/edgelabels.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/meta_taxa.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/meta_types.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/nexml.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/phenoscape.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/sets.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/taxa.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/timetree.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/tolweb.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/treebase-record.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/trees-uris.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeXML/trees.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeXML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeuralNetwork
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeuralNetwork/enolase.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeuralNetwork
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/NeuralNetwork/repeat.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/NeuralNetwork
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/ByteOrderMarkFile.nwk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/bats.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/codonposset.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/int_node_labels.nwk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/test.new -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/test_Nexus_input.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/vSysLab_Ganaspidium_multistate.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/vSysLab_Heptascelio_no-states_10+chars.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nexus/vSysLab_Oreiscelio_discrete+continuous.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nexus
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nib/test_even.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nib/test_even_bigendian.nib -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nib/test_even_littleendian.nib -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nib/test_odd.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nib/test_odd_bigendian.nib -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Nib/test_odd_littleendian.nib -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Nib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Alignments/aa_alignment.phylip -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Alignments/alignment.phylip -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Alignments/dottednames.phylip -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Alignments/dottednum.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Alignments/longnames.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Alignments/lysinYangSwanson2002.nuc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Alignments
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/bad1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/bad2.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/bad3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/SE.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/alpha1rho1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/baseml.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model0.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model2.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model4.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model5.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model6.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model7.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/model8.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/nhomo1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/nhomo3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/nhomo4.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/nparK1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/nparK2.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/nparK3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/baseml/nparK4.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/baseml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/NSsite3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/SE.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/aa_model0.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/aa_pairwise.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/all_NSsites.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/branchsiteA.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/clademodelC.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/codeml.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/freeratio.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/m2a_rel.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/ngene2_mgene02.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/ngene2_mgene1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/ngene2_mgene34.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/codeml/pairwise.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/species.tree -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/yn00.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/yn00/yn00.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/yn00/yn00_dotted.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/yn00/yn00_dottednum.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Control_files/yn00/yn00_long.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Control_files/yn00
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/bad_results.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/SE/SE-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/SE/SE-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/SE/SE-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/SE/SE-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/SE/SE-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/SE/SE-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/SE/SE-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/SE
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/alpha1rho1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/alpha1rho1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/alpha1rho1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/alpha1rho1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/baseml_SE.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/baseml_alpha1rho1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model0-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model0-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model0-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model0-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model0-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model0-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model0-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model1-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model1-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model1-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model1-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model1-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model1-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model1-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model2-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model2-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model2-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model2-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model2-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model2-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model2-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model3-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model3-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model3-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model3-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model3-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model3-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model3-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model4-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model4-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model4-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model4-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model4-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model4-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model4-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model5-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model5-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model5-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model5-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model5-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model5-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model5-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model6-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model6-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model6-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model6-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model6-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model6-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model6-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model7-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model7-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model7-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model7-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model7-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model7-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model7-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model8-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model8-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model8-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model8-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model8-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model8-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/model/model8-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/model
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nhomo
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK1-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK1-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK1-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK2-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK2-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK2-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK3-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK3-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK3-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK4-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK4-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/nparK/nparK4-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/nparK
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/versions
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/versions/baseml41.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/versions
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/versions/baseml43.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/versions
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/versions/baseml44.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/versions
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/baseml/versions/baseml44c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/baseml/versions
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/NSsite3
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/SE/SE-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/SE/SE-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/SE/SE-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/SE/SE-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/SE/SE-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/SE/SE-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/SE/SE-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/SE
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_model0
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/all_NSsites
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/branchsiteA
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/clademodelC
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/freeratio
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/m2a_rel
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/m2a_rel
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/m2a_rel
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_8.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/m2a_rel
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_9a.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/m2a_rel
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/codeml/tree_regexp_versatility.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/codeml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00-4_8.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00_dotted-4_9i.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00_dottednum-4_9i.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Results/yn00/yn00_long-4_8.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Results/yn00
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Trees/bad.tree -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Trees/lysin.trees -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Trees/lysin.trees.4.6 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/Trees/species.tree -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PAML/gen_results.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1A7G.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1A8O.asa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1A8O.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1A8O.mmtf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1A8O.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1A8O.rsa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1A8O.xyzr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1AS5.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1LCD.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1LCD.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1MOM_min.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1SSU_mod.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/1SSU_mod.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/2BEG.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/2BEG.dssp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/2BEG.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/2BEG_noheader.dssp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/2OFG.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/2XHE.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/2XHE.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/2n0n_M1.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/3JQH.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/4CUP.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/4CUP.mmtf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/4Q9R_min.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/4ZHL.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/4ZHL.mmtf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/6WQA.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/7CFN.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/7CFN_aligned.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/7DDO.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/Ahmad_RASA.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/Miller_RASA.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/Sander_RASA.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/Wilke_RASA.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/a_structure.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/a_structure.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/alignment_file.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/d256ba_.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/disordered.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/dssp_xtra_Sander.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/header.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/ions.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/lib_10_z_5.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PDB/occupancy.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PDB
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PQR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PQR/1A80.pqr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PQR
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phd
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phd/phd1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phd
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phd/phd2 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phd
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phd/phd_454 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phd
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phd/phd_solexa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phd
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/five.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/four.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/hennigian.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/horses.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/horses.tree -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/interlaced.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/interlaced2.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/one.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/random.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/reference_dna.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/reference_dna2.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/sequential.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/sequential2.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/six.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/three.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Phylip/two.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Phylip
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PhyloXML/apaf.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PhyloXML/bcl_2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PhyloXML/distribution.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PhyloXML/example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PhyloXML/made_up.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PhyloXML/o_tol_332_d_dollo.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PhyloXML/phyloxml_examples.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PhyloXML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/big.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/c2line.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/c2space.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/c3line.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/c3space.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/haplo.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/haplo2.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/PopGen/haplo3.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PopGen
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00100.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00113.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00144.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00149.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00340.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00424.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00472.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00640.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00787.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/pdoc00933.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/Doc/prosite.excerpt.doc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/ps00107.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/ps00159.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/ps00165.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/ps00432.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/ps00488.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Prosite/ps00546.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Prosite
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_diff_ids.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_double_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_double_seq.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_long_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_no_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_qual_del.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_qual_escape.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_qual_null.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_qual_space.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_qual_tab.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_qual_unit_sep.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_qual_vtab.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_short_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_spaces.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_tabs.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_trunc_at_plus.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_trunc_at_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_trunc_at_seq.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_trunc_in_plus.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_trunc_in_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_trunc_in_seq.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/error_trunc_in_title.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/example.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/example.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/example.fastq.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/example.fastq.gz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/example.qual -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/example_dos.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/example_dos.fastq.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/illumina_faked.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/illumina_full_range_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/illumina_full_range_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/illumina_full_range_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/illumina_full_range_original_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/longreads_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/longreads_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/longreads_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/longreads_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/misc_dna_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/misc_dna_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/misc_dna_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/misc_dna_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/misc_rna_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/misc_rna_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/misc_rna_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/misc_rna_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/sanger_93.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/sanger_faked.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/sanger_full_range_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/sanger_full_range_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/sanger_full_range_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/sanger_full_range_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/solexa_example.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/solexa_faked.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/solexa_full_range_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/solexa_full_range_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/solexa_full_range_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/solexa_full_range_original_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/tricky.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/wrapping_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/wrapping_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/wrapping_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/wrapping_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Quality/zero_length.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Quality
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/bamii.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/bamii.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/cac81.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/cac81.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/crei.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/crei.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/foki.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/foki.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/pvuii.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/pvuii.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/taqi.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Rebase/taqi.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Rebase
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Registry
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Registry/EDD_RAT.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Registry
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Registry/bt001 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Registry
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Registry/seqs.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Registry
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_alt_index_at_end.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_alt_index_at_start.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_alt_index_in_middle.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_index_at_start.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_index_in_middle.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_no_manifest.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_random_10_reads.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_random_10_reads.qual -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_random_10_reads.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_random_10_reads.sff.gz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_random_10_reads_no_trim.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/E3MFGYR02_random_10_reads_no_trim.qual -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/greek.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/invalid_greek_E3MFGYR02.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/invalid_paired_E3MFGYR02.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/paired.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/triple_sff.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Roche/triple_sff_rel_paths.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Roche
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/dir.cla.scop.txt_test -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/dir.des.scop.txt_test -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/dir.hie.scop.txt_test -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/raftest.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-all-test.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-10-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-100-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-20-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-25-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-30-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-35-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-40-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-50-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-70-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-90-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-95-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+0,7-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+0-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+1-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-0,3-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-1,3-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-1-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-10-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-15-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-2,3-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-2-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-20-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-25-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-3-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-4-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-5-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-50-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SCOP/testDom.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SCOP
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Saf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Saf/saf1.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Saf
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/bam1.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/bam1_sorted.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/bam2.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/bam2_sorted.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/ex1.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/ex1.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/ex1.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/ex1_header.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/ex1_header.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/ex1_refresh.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/readme.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/sam1.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SamBam/sam2.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SamBam
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SeqXML/corrupt_example1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SeqXML/corrupt_example2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SeqXML/dna_example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SeqXML/global_species_example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SeqXML/protein_example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SeqXML/rna_example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SeqXML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SnapGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SnapGene/pFA-KanMX4.dna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SnapGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SnapGene/sample-d.dna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SnapGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SnapGene/sample-e.dna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SnapGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SnapGene/sample-f.dna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SnapGene
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/cath1.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/cath2.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/cath3.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/example.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/funny.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/globins45.ali -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam1.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam2.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam3.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam4.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam5.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam6.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam7.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam8.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/pfam9.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/rfam1.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/rfam2.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/rfam3.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/rfam4.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/rfam5.seed.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Stockholm/simple.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Stockholm
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SubsMat/aaDistrib.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SubsMat/acc_rep_mat.pik -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SubsMat/protein_count.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SubsMat/protein_freq.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SubsMat/redAADistrib.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SubsMat/redAltAADistrib.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SubsMat
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/F2CXE6.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/F2CXE6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/H2CNN8.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/H2CNN8.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/O23729.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/O95832.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P04439.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P0A186.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P0CK95.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P16235.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P39896.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P60137.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P60904.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P62258.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P68308.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P84001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/P97881.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/Q13454.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/Q13639.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/Q13639.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/Q7Z739.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/R5HY77.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/keywlist.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/keywlist2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/multi_ex.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/multi_ex.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/multi_ex.list -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/multi_ex.rdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/multi_ex.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/multi_ex.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/sp012 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/sp013 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/sp015 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/sp016 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/uni001 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/uni002 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/SwissProt/uni003 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/SwissProt
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/adam_refs.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/consensus_refs.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/majority_ref.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/msa.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/neighbor_trees.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/nj.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/nj_min.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/pars3.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/strict_refs.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/test.log -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/trees.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TreeConstruction/upgma.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TreeConstruction
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TwoBit
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TwoBit/sequence.bigendian.2bit -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TwoBit
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TwoBit/sequence.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TwoBit
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TwoBit/sequence.littleendian.2bit -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TwoBit
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/TwoBit/sequence.long.2bit -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/TwoBit
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/UniGene/Eca.1.2425.data -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/UniGene/Hs.2.data -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/UniGene/Mdm_partial.data -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniGene
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/UniProt/gene_association.goa_yeast.1.gaf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/UniProt/goa_human_sample.gpi -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/UniProt/goa_yeast.gaf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/UniProt/goa_yeast.gpa.59.gpa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/UniProt/gp_information.goa_yeast.28.gpi -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/UniProt
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Wise/human_114_g01_exons.fna_01 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Wise/human_114_g02_exons.fna_01 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Wise
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Xdna
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Xdna/sample-a.xdna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Xdna
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Xdna/sample-b.xdna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Xdna
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/Xdna/sample-c.xprt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/Xdna
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/biosql.ini.appveyor -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/biosql.ini.sample -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/adh.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/drosophilla.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/egfr_id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/egfr_nucl.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/egfr_pro.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/nucl1.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/nucl2.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/nucl3.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/nucl4.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/nucl5.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/pro1.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/pro2.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/pro3.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/pro4.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/codonalign/pro5.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/common_BioSQL.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/common_BioSQL_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/Arnt.sites -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/MA0056.1.transfac -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/REB1.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/SRF.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/abdb.xms -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/alignace.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/clusterbuster.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/clusterbuster.pfm.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/fourcolumns.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/fourrows.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/mast.Klf1-200.cd.oops.xml.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/mast.Klf1-200.cd.oops.xml.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/mast.adh.de.oops.html.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/mast.adh.de.oops.html.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/mast.crp0.de.oops.txt.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/mast.crp0.de.oops.txt.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/meme.INO_up800.classic.oops.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/meme.adh.classic.oops.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/meme.farntrans5.classic.anr.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/meme.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/meme.psp_test.classic.zoops.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/minimal_test.meme -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/motifs/transfac.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/motifs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/msf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/msf/DOA_prot.msf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/msf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/msf/W_prot.msf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/msf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/pairwise2_testCases.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/phenotype/BadPlate.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/phenotype/Plate.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/phenotype/Plate_2.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/phenotype/Plates.csv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/phenotype/SmallPlate.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/phenotype/SmallPlate_2.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/phenotype/SmallPlates.csv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/requires_internet.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/search_tests_common.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/seq_tests_common.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Ace.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Affy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_AlignIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_AlignIO_ClustalIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_AlignIO_EmbossIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_AlignIO_FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_AlignIO_MauveIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_AlignIO_PhylipIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_AlignIO_convert.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_AlignInfo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_Alignment.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_a2m.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_bed.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_bigbed.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_bigmaf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_bigpsl.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_clustal.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_emboss.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_exonerate.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_fasta.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_hhr.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_maf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_mauve.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_msf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_nexus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_phylip.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_psl.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_sam.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_stockholm.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Align_tabular.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Application.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_BWA_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_BioSQL_MySQLdb_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_BioSQL_mysql_connector.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_BioSQL_mysql_connector_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_BioSQL_psycopg2_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_BioSQL_sqlite3.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_BioSQL_sqlite3_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Blast_Record.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_CAPS.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Chi2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_ClustalOmega_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Clustalw_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Cluster.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_CodonTable.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_ColorSpiral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Compass.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Consensus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Dialign_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_EMBL_unittest.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Emboss.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_EmbossPrimer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Entrez_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Entrez_parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Enzyme.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_ExPASy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Fasttree_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_File.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_GenBank.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_GenomeDiagram.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_GraphicsChromosome.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_GraphicsDistribution.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_GraphicsGeneral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_HMMCasino.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_HMMGeneral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_KEGG.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_KEGG_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_KGML_graphics.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_KGML_graphics_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_KGML_nographics.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_KeyWList.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_LogisticRegression.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_MafIO_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Mafft_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_MarkovModel.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Medline.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_NCBITextParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_NCBIXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_NCBI_BLAST_tools.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_NCBI_qblast.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_NMR.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_NaiveBayes.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Nexus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PAML_baseml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PAML_codeml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PAML_yn00.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDBList.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_CEAligner.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_DSSP.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_Dice.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_Disordered.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_Exposure.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_FragmentMapper.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_KDTree.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_MMCIF2Dict.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_MMCIFIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_MMCIFParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_NACCESS.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_PDBIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_PDBParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_PSEA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_Polypeptide.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_QCSuperimposer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_SASA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_SMCRA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_Selection.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_StructureAlignment.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_Superimposer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_internal_coords.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_parse_pdb_header.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_vectors.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PQR.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Pathway.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Phd.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Phylo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PhyloXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Phylo_CDAO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Phylo_NeXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Phylo_matplotlib.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Phylo_networkx.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PopGen_GenePop_nodepend.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Prank_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Probcons_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_ProtParam.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_RCSBFormats.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Restriction.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_Astral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_Cla.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_Des.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_Dom.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_Hie.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_Raf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_Residues.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_Scop.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SCOP_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SVDSuperimposer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_blast_tab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_blast_tab_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_blast_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_blast_xml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_blast_xml_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_blat_psl.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_blat_psl_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_exonerate.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_exonerate_text_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_exonerate_vulgar_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_fasta_m10.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_fasta_m10_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hhsuite2_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hmmer2_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hmmer2_text_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hmmer3_domtab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hmmer3_domtab_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hmmer3_tab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hmmer3_tab_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hmmer3_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_hmmer3_text_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_interproscan_xml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_legacy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_model.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SearchIO_write.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqFeature.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_AbiIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_Gck.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_Insdc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_NibIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_PdbIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_QualityIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_SeqXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_SnapGene.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_TwoBitIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_Xdna.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_features.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO_write.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqRecord.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqUtils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Seq_objs.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SffIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SwissProt.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_TCoffee_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_TogoWS.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_TreeConstruction.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Tutorial.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_UniGene.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_UniProt_GOA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Uniprot.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Wise.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_align.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_align_substitution_matrices.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_bgzf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_cellosaurus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_codonalign.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_geo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_kNN.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_motifs.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_motifs_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_pairwise2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_pairwise2_no_C.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_pairwise_aligner.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_pairwise_alignment_map.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_phenotype.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_phenotype_fit.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_phyml_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_prodoc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_prosite.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_samtools_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_seq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_translate.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Muscle_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/run_tests.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Entrez.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/requires_internet.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Ace.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Affy.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_AlignIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_AlignIO_ClustalIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_AlignIO_EmbossIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_AlignIO_FastaIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_AlignIO_MauveIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_AlignIO_PhylipIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_AlignIO_convert.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_AlignInfo.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_Alignment.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_a2m.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_bed.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_bigbed.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_bigmaf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_bigpsl.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_clustal.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_emboss.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_exonerate.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_fasta.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_hhr.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_maf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_mauve.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_msf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_nexus.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_phylip.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_psl.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_sam.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_stockholm.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Align_tabular.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Application.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_BWA_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_BioSQL_MySQLdb_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/common_BioSQL.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/seq_tests_common.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/common_BioSQL_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_BioSQL_mysql_connector.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_BioSQL_mysql_connector_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_BioSQL_psycopg2_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_BioSQL_sqlite3.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_BioSQL_sqlite3_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Blast_Record.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_CAPS.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Chi2.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_ClustalOmega_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Clustalw_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Cluster.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_CodonTable.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_ColorSpiral.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Compass.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Consensus.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Dialign_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_EMBL_unittest.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Emboss.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_EmbossPrimer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Entrez.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Entrez_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Entrez_parser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Enzyme.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_ExPASy.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Fasttree_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_File.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_GenBank.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_GenomeDiagram.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_GraphicsChromosome.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_GraphicsDistribution.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_GraphicsGeneral.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_HMMCasino.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_HMMGeneral.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_KEGG.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_KEGG_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_KGML_graphics.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_KGML_graphics_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_KGML_nographics.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_KeyWList.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_LogisticRegression.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_MafIO_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Mafft_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_MarkovModel.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Medline.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Muscle_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_NCBITextParser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_NCBIXML.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_NCBI_BLAST_tools.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_NCBI_qblast.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_NMR.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_NaiveBayes.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Nexus.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PAML_baseml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PAML_codeml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PAML_yn00.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDBList.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_CEAligner.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_DSSP.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_Dice.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_Disordered.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_Exposure.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_FragmentMapper.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_KDTree.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_MMCIF2Dict.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_MMCIFIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_MMCIFParser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_NACCESS.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_PDBIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_PDBParser.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_PSEA.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_Polypeptide.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_QCSuperimposer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_SASA.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_SMCRA.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_Selection.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_StructureAlignment.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_Superimposer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_internal_coords.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_parse_pdb_header.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PDB_vectors.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PQR.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Pathway.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Phd.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Phylo.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PhyloXML.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Phylo_CDAO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Phylo_NeXML.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Phylo_matplotlib.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Phylo_networkx.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_PopGen_GenePop_nodepend.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Prank_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Probcons_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_ProtParam.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_RCSBFormats.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Restriction.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_Astral.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_Cla.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_Des.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_Dom.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_Hie.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_Raf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_Residues.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_Scop.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SCOP_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SVDSuperimposer.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_blast_tab.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_blast_tab_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/search_tests_common.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_blast_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_blast_xml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_blast_xml_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_blat_psl.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_blat_psl_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_exonerate.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_exonerate_text_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_exonerate_vulgar_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_fasta_m10.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_fasta_m10_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hhsuite2_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hmmer2_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hmmer2_text_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hmmer3_domtab.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hmmer3_domtab_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hmmer3_tab.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hmmer3_tab_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hmmer3_text.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_hmmer3_text_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_interproscan_xml.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_legacy.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_model.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SearchIO_write.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqFeature.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_AbiIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_FastaIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_Gck.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_Insdc.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_NibIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_PdbIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_QualityIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_SeqXML.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_SnapGene.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_TwoBitIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_Xdna.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_features.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_index.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqIO_write.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqRecord.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SeqUtils.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Seq_objs.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SffIO.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_SwissProt.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_TCoffee_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_TogoWS.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_TreeConstruction.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Tutorial.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_UniGene.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_UniProt_GOA.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Uniprot.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_Wise.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_align.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_align_substitution_matrices.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_bgzf.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_cellosaurus.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_codonalign.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_geo.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_kNN.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_motifs.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_motifs_online.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_pairwise2.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/pairwise2_testCases.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_pairwise2_no_C.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_pairwise_aligner.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_pairwise_alignment_map.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_phenotype.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_phenotype_fit.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_phyml_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_prodoc.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_prosite.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_samtools_tool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_seq.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/__pycache__/test_translate.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/output.best.fas -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/output.best.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/tmpdirprankmsaEfBlrr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/tmpdirprankmsa0F2xsN
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/out.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/tree1.nwk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/other_trees.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/tree1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/other_trees.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/File.py to File.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/MarkovModel.py to MarkovModel.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Seq.py to Seq.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqFeature.py to SeqFeature.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqRecord.py to SeqRecord.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/_utils.py to _utils.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/bgzf.py to bgzf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/kNN.py to kNN.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/pairwise2.py to pairwise2.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy/CelFile.py to CelFile.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Affy/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/a2m.py to a2m.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/bed.py to bed.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/bigbed.py to bigbed.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/bigmaf.py to bigmaf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/bigpsl.py to bigpsl.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/clustal.py to clustal.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/emboss.py to emboss.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/exonerate.py to exonerate.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/fasta.py to fasta.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/hhr.py to hhr.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/interfaces.py to interfaces.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/maf.py to maf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/mauve.py to mauve.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/msf.py to msf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/nexus.py to nexus.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/phylip.py to phylip.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/psl.py to psl.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/sam.py to sam.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/stockholm.py to stockholm.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/tabular.py to tabular.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_ClustalOmega.py to _ClustalOmega.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Clustalw.py to _Clustalw.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Dialign.py to _Dialign.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_MSAProbs.py to _MSAProbs.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Mafft.py to _Mafft.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Prank.py to _Prank.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Probcons.py to _Probcons.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_TCoffee.py to _TCoffee.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/Applications/_Muscle.py to _Muscle.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/AlignIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Alphabet/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Application/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/Applications.py to Applications.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/ParseBlastTable.py to ParseBlastTable.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/Record.py to Record.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Blast/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/CAPS/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Cluster/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/codonalign/codonseq.py to codonseq.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Compass/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/CodonTable.py to CodonTable.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/IUPACData.py to IUPACData.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/PDBData.py to PDBData.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/SCOPData.py to SCOPData.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Data/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/Applications.py to Applications.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/Primer3.py to Primer3.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Emboss/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/Parser.py to Parser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Entrez/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/Record.py to Record.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/Scanner.py to Scanner.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/GenBank/utils.py to utils.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo/Record.py to Record.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Geo/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/Comparative.py to Comparative.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/Distribution.py to Distribution.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/DynamicProgramming.py to DynamicProgramming.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/MarkovModel.py to MarkovModel.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/Trainer.py to Trainer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/Utilities.py to Utilities.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/HMM/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/REST.py to REST.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Compound/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Enzyme/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Gene/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/Map/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/KGML_parser.py to KGML_parser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/KGML_pathway.py to KGML_pathway.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/KEGG/KGML/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/DefaultParser.py to DefaultParser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmtf/mmtfio.py to mmtfio.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/AbstractPropertyMap.py to AbstractPropertyMap.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Atom.py to Atom.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Chain.py to Chain.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/DSSP.py to DSSP.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Dice.py to Dice.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Entity.py to Entity.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/FragmentMapper.py to FragmentMapper.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/HSExposure.py to HSExposure.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/MMCIF2Dict.py to MMCIF2Dict.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/MMCIFParser.py to MMCIFParser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Model.py to Model.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/NACCESS.py to NACCESS.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/NeighborSearch.py to NeighborSearch.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PDBExceptions.py to PDBExceptions.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PDBIO.py to PDBIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PDBList.py to PDBList.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PDBParser.py to PDBParser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PICIO.py to PICIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/PSEA.py to PSEA.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Polypeptide.py to Polypeptide.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Residue.py to Residue.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/ResidueDepth.py to ResidueDepth.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/SASA.py to SASA.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/SCADIO.py to SCADIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Selection.py to Selection.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Structure.py to Structure.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/StructureAlignment.py to StructureAlignment.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/StructureBuilder.py to StructureBuilder.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/Superimposer.py to Superimposer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/cealign.py to cealign.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/ic_data.py to ic_data.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/ic_rebuild.py to ic_rebuild.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/internal_coords.py to internal_coords.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/mmcifio.py to mmcifio.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/parse_pdb_header.py to parse_pdb_header.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/qcprot.py to qcprot.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/vectors.py to vectors.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PDB/QCPSuperimposer/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Medline/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/alignace.py to alignace.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/clusterbuster.py to clusterbuster.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/mast.py to mast.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/matrix.py to matrix.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/meme.py to meme.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/minimal.py to minimal.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/pfm.py to pfm.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/thresholds.py to thresholds.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/transfac.py to transfac.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/xms.py to xms.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/applications/_xxmotif.py to _xxmotif.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/motifs/jaspar/db.py to db.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/Nexus.py to Nexus.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/Nodes.py to Nodes.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/StandardData.py to StandardData.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/Trees.py to Trees.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Nexus/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/NOEtools.py to NOEtools.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/NMR/xpktools.py to xpktools.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/Graph.py to Graph.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/MultiGraph.py to MultiGraph.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Pathway/Rep/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/Controller.py to Controller.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/PrintFormat.py to PrintFormat.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/Restriction.py to Restriction.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Restriction/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Cla.py to Cla.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Des.py to Des.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Dom.py to Dom.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Hie.py to Hie.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Raf.py to Raf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/Residues.py to Residues.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SCOP/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_index.py to _index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_utils.py to _utils.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/NCBIStandalone.py to NCBIStandalone.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/ParserSupport.py to ParserSupport.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_legacy/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/_base.py to _base.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/hit.py to hit.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/_model/query.py to query.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/blast_text.py to blast_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py to hhsuite2_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqIO/_index.py to _index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SeqUtils/lcc.py to lcc.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Ace.py to Ace.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Phd.py to Phd.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/SwissProt/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/TogoWS/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/CDAO.py to CDAO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Consensus.py to Consensus.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/NeXML.py to NeXML.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Newick.py to Newick.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/_io.py to _io.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/_utils.py to _utils.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniGene/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt/GOA.py to GOA.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/UniProt/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/dnal.py to dnal.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Bio/Wise/psw.py to psw.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/BioSeq.py to BioSeq.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/DBUtils.py to DBUtils.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/Loader.py to Loader.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/BioSQL/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/ACT_example.py to ACT_example.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/Proux_et_al_2002_Figure_6.py to Proux_et_al_2002_Figure_6.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/clustal_run.py to clustal_run.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/fasta_dictionary.py to fasta_dictionary.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/fasta_iterator.py to fasta_iterator.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/nmr/simplepredict.py to simplepredict.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/swissprot.py to swissprot.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Doc/examples/www_blast.py to www_blast.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/PAML/gen_results.py to gen_results.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/common_BioSQL.py to common_BioSQL.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/common_BioSQL_online.py to common_BioSQL_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/pairwise2_testCases.py to pairwise2_testCases.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/requires_internet.py to requires_internet.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/search_tests_common.py to search_tests_common.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/seq_tests_common.py to seq_tests_common.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Ace.py to test_Ace.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Affy.py to test_Affy.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_AlignIO.py to test_AlignIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_AlignIO_ClustalIO.py to test_AlignIO_ClustalIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_AlignIO_EmbossIO.py to test_AlignIO_EmbossIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_AlignIO_FastaIO.py to test_AlignIO_FastaIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_AlignIO_MauveIO.py to test_AlignIO_MauveIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_AlignIO_PhylipIO.py to test_AlignIO_PhylipIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_AlignIO_convert.py to test_AlignIO_convert.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_AlignInfo.py to test_AlignInfo.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_Alignment.py to test_Align_Alignment.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_a2m.py to test_Align_a2m.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_bed.py to test_Align_bed.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_bigbed.py to test_Align_bigbed.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_bigmaf.py to test_Align_bigmaf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_bigpsl.py to test_Align_bigpsl.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_clustal.py to test_Align_clustal.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_emboss.py to test_Align_emboss.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_exonerate.py to test_Align_exonerate.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_fasta.py to test_Align_fasta.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_hhr.py to test_Align_hhr.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_maf.py to test_Align_maf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_mauve.py to test_Align_mauve.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_msf.py to test_Align_msf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_nexus.py to test_Align_nexus.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_phylip.py to test_Align_phylip.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_psl.py to test_Align_psl.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_sam.py to test_Align_sam.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_stockholm.py to test_Align_stockholm.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Align_tabular.py to test_Align_tabular.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Application.py to test_Application.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_BWA_tool.py to test_BWA_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_BioSQL_MySQLdb_online.py to test_BioSQL_MySQLdb_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_BioSQL_mysql_connector.py to test_BioSQL_mysql_connector.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_BioSQL_mysql_connector_online.py to test_BioSQL_mysql_connector_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_BioSQL_psycopg2_online.py to test_BioSQL_psycopg2_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_BioSQL_sqlite3.py to test_BioSQL_sqlite3.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_BioSQL_sqlite3_online.py to test_BioSQL_sqlite3_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Blast_Record.py to test_Blast_Record.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_CAPS.py to test_CAPS.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Chi2.py to test_Chi2.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_ClustalOmega_tool.py to test_ClustalOmega_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Clustalw_tool.py to test_Clustalw_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Cluster.py to test_Cluster.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_CodonTable.py to test_CodonTable.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_ColorSpiral.py to test_ColorSpiral.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Compass.py to test_Compass.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Consensus.py to test_Consensus.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Dialign_tool.py to test_Dialign_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_EMBL_unittest.py to test_EMBL_unittest.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Emboss.py to test_Emboss.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_EmbossPrimer.py to test_EmbossPrimer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Entrez_online.py to test_Entrez_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Entrez_parser.py to test_Entrez_parser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Enzyme.py to test_Enzyme.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_ExPASy.py to test_ExPASy.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Fasttree_tool.py to test_Fasttree_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_File.py to test_File.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_GenBank.py to test_GenBank.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_GenomeDiagram.py to test_GenomeDiagram.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_GraphicsChromosome.py to test_GraphicsChromosome.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_GraphicsDistribution.py to test_GraphicsDistribution.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_GraphicsGeneral.py to test_GraphicsGeneral.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_HMMCasino.py to test_HMMCasino.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_HMMGeneral.py to test_HMMGeneral.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_KEGG.py to test_KEGG.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_KEGG_online.py to test_KEGG_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_KGML_graphics.py to test_KGML_graphics.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_KGML_graphics_online.py to test_KGML_graphics_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_KGML_nographics.py to test_KGML_nographics.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_KeyWList.py to test_KeyWList.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_LogisticRegression.py to test_LogisticRegression.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_MafIO_index.py to test_MafIO_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Mafft_tool.py to test_Mafft_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_MarkovModel.py to test_MarkovModel.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Medline.py to test_Medline.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_NCBITextParser.py to test_NCBITextParser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_NCBIXML.py to test_NCBIXML.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_NCBI_BLAST_tools.py to test_NCBI_BLAST_tools.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_NCBI_qblast.py to test_NCBI_qblast.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_NMR.py to test_NMR.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_NaiveBayes.py to test_NaiveBayes.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Nexus.py to test_Nexus.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PAML_baseml.py to test_PAML_baseml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PAML_codeml.py to test_PAML_codeml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PAML_yn00.py to test_PAML_yn00.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDBList.py to test_PDBList.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_CEAligner.py to test_PDB_CEAligner.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_DSSP.py to test_PDB_DSSP.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_Dice.py to test_PDB_Dice.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_Disordered.py to test_PDB_Disordered.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_Exposure.py to test_PDB_Exposure.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_FragmentMapper.py to test_PDB_FragmentMapper.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_KDTree.py to test_PDB_KDTree.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_MMCIF2Dict.py to test_PDB_MMCIF2Dict.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_MMCIFIO.py to test_PDB_MMCIFIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_MMCIFParser.py to test_PDB_MMCIFParser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_NACCESS.py to test_PDB_NACCESS.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_PDBIO.py to test_PDB_PDBIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_PDBParser.py to test_PDB_PDBParser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_PSEA.py to test_PDB_PSEA.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_Polypeptide.py to test_PDB_Polypeptide.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_QCSuperimposer.py to test_PDB_QCSuperimposer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_SASA.py to test_PDB_SASA.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_SMCRA.py to test_PDB_SMCRA.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_Selection.py to test_PDB_Selection.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_StructureAlignment.py to test_PDB_StructureAlignment.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_Superimposer.py to test_PDB_Superimposer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_internal_coords.py to test_PDB_internal_coords.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_parse_pdb_header.py to test_PDB_parse_pdb_header.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PDB_vectors.py to test_PDB_vectors.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PQR.py to test_PQR.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Pathway.py to test_Pathway.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Phd.py to test_Phd.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Phylo.py to test_Phylo.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PhyloXML.py to test_PhyloXML.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Phylo_CDAO.py to test_Phylo_CDAO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Phylo_NeXML.py to test_Phylo_NeXML.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Phylo_matplotlib.py to test_Phylo_matplotlib.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Phylo_networkx.py to test_Phylo_networkx.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_PopGen_GenePop_nodepend.py to test_PopGen_GenePop_nodepend.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Prank_tool.py to test_Prank_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Probcons_tool.py to test_Probcons_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_ProtParam.py to test_ProtParam.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_RCSBFormats.py to test_RCSBFormats.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Restriction.py to test_Restriction.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_Astral.py to test_SCOP_Astral.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_Cla.py to test_SCOP_Cla.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_Des.py to test_SCOP_Des.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_Dom.py to test_SCOP_Dom.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_Hie.py to test_SCOP_Hie.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_Raf.py to test_SCOP_Raf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_Residues.py to test_SCOP_Residues.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_Scop.py to test_SCOP_Scop.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SCOP_online.py to test_SCOP_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SVDSuperimposer.py to test_SVDSuperimposer.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_blast_tab.py to test_SearchIO_blast_tab.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_blast_tab_index.py to test_SearchIO_blast_tab_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_blast_text.py to test_SearchIO_blast_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_blast_xml.py to test_SearchIO_blast_xml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_blast_xml_index.py to test_SearchIO_blast_xml_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_blat_psl.py to test_SearchIO_blat_psl.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_blat_psl_index.py to test_SearchIO_blat_psl_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_exonerate.py to test_SearchIO_exonerate.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_exonerate_text_index.py to test_SearchIO_exonerate_text_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_exonerate_vulgar_index.py to test_SearchIO_exonerate_vulgar_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_fasta_m10.py to test_SearchIO_fasta_m10.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_fasta_m10_index.py to test_SearchIO_fasta_m10_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hhsuite2_text.py to test_SearchIO_hhsuite2_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hmmer2_text.py to test_SearchIO_hmmer2_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hmmer2_text_index.py to test_SearchIO_hmmer2_text_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hmmer3_domtab.py to test_SearchIO_hmmer3_domtab.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hmmer3_domtab_index.py to test_SearchIO_hmmer3_domtab_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hmmer3_tab.py to test_SearchIO_hmmer3_tab.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hmmer3_tab_index.py to test_SearchIO_hmmer3_tab_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hmmer3_text.py to test_SearchIO_hmmer3_text.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_hmmer3_text_index.py to test_SearchIO_hmmer3_text_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_interproscan_xml.py to test_SearchIO_interproscan_xml.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_legacy.py to test_SearchIO_legacy.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_model.py to test_SearchIO_model.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SearchIO_write.py to test_SearchIO_write.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqFeature.py to test_SeqFeature.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO.py to test_SeqIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_AbiIO.py to test_SeqIO_AbiIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_FastaIO.py to test_SeqIO_FastaIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_Gck.py to test_SeqIO_Gck.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_Insdc.py to test_SeqIO_Insdc.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_NibIO.py to test_SeqIO_NibIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_PdbIO.py to test_SeqIO_PdbIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_QualityIO.py to test_SeqIO_QualityIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_SeqXML.py to test_SeqIO_SeqXML.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_SnapGene.py to test_SeqIO_SnapGene.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_TwoBitIO.py to test_SeqIO_TwoBitIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_Xdna.py to test_SeqIO_Xdna.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_features.py to test_SeqIO_features.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_index.py to test_SeqIO_index.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_online.py to test_SeqIO_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqIO_write.py to test_SeqIO_write.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqRecord.py to test_SeqRecord.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SeqUtils.py to test_SeqUtils.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Seq_objs.py to test_Seq_objs.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SffIO.py to test_SffIO.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_SwissProt.py to test_SwissProt.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_TCoffee_tool.py to test_TCoffee_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_TogoWS.py to test_TogoWS.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_TreeConstruction.py to test_TreeConstruction.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Tutorial.py to test_Tutorial.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_UniGene.py to test_UniGene.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_UniProt_GOA.py to test_UniProt_GOA.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Uniprot.py to test_Uniprot.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Wise.py to test_Wise.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_align.py to test_align.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_align_substitution_matrices.py to test_align_substitution_matrices.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_bgzf.py to test_bgzf.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_cellosaurus.py to test_cellosaurus.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_codonalign.py to test_codonalign.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_geo.py to test_geo.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_kNN.py to test_kNN.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_motifs.py to test_motifs.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_motifs_online.py to test_motifs_online.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_pairwise2.py to test_pairwise2.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_pairwise2_no_C.py to test_pairwise2_no_C.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_pairwise_aligner.py to test_pairwise_aligner.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_pairwise_alignment_map.py to test_pairwise_alignment_map.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_phenotype.py to test_phenotype.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_phenotype_fit.py to test_phenotype_fit.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_phyml_tool.py to test_phyml_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_prodoc.py to test_prodoc.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_prosite.py to test_prosite.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_samtools_tool.py to test_samtools_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_seq.py to test_seq.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_translate.py to test_translate.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Muscle_tool.py to test_Muscle_tool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/run_tests.py to run_tests.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Tests/test_Entrez.py to test_Entrez.cpython-311.pyc
running install_egg_info
Copying biopython.egg-info to /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/biopython-1.81.egg-info
Skipping SOURCES.txt
running install_scripts
dh_numpy3 -ppython3-biopython
	mv debian/python3-biopython.substvars.new debian/python3-biopython.substvars
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython//usr/lib/python3.11/dist-packages
	cp --reflink=auto -a debian/tmp/usr/lib/python3.11/dist-packages/Bio debian/tmp/usr/lib/python3.11/dist-packages/biopython-1.81.egg-info debian/python3-biopython//usr/lib/python3.11/dist-packages/
   dh_installdocs -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/usr/share/doc/python3-biopython
	install -m0755 -d debian/python3-biopython/usr/share/doc/python3-biopython
	cp --reflink=auto -a ./CONTRIB.rst debian/python3-biopython/usr/share/doc/python3-biopython
	cp --reflink=auto -a ./CONTRIBUTING.rst debian/python3-biopython/usr/share/doc/python3-biopython
	cp --reflink=auto -a ./DEPRECATED.rst debian/python3-biopython/usr/share/doc/python3-biopython
	cp --reflink=auto -a ./NEWS.rst debian/python3-biopython/usr/share/doc/python3-biopython
	chmod -R u\+rw,go=rX debian/python3-biopython/usr/share/doc
	install -p -m0644 debian/README.Debian debian/python3-biopython/usr/share/doc/python3-biopython/README.Debian
	install -p -m0644 debian/copyright debian/python3-biopython/usr/share/doc/python3-biopython/copyright
   dh_installchangelogs -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/usr/share/doc/python3-biopython
	install -p -m0644 debian/.debhelper/generated/python3-biopython/dh_installchangelogs.dch.trimmed debian/python3-biopython/usr/share/doc/python3-biopython/changelog.Debian
	install -p -m0644 debian/.debhelper/generated/python3-biopython/dh_installchangelogs.news.trimmed debian/python3-biopython/usr/share/doc/python3-biopython/NEWS.Debian
   dh_python3 -a -O--buildsystem=pybuild
D: dh_python3 dh_python3:179: version: 6.20231107
D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '-a', '-O--buildsystem=pybuild']
D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=True, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild'])
D: dh_python3 dh_python3:182: supported Python versions: 3.11 (default=3.11)
D: dh_python3 debhelper:149: skipping package: python-biopython-doc
D: dh_python3 debhelper:183: source=python-biopython, binary packages=['python3-biopython']
D: dh_python3 dh_python3:204: processing package python3-biopython...
D: dh_python3 fs:50: moving files from debian/python3-biopython/usr/lib/python3.11/dist-packages to debian/python3-biopython/usr/lib/python3/dist-packages/
D: dh_python3 fs:341: package python3-biopython details = {'requires.txt': {'debian/python3-biopython/usr/lib/python3/dist-packages/biopython-1.81.egg-info/requires.txt'}, 'egg-info': {'debian/python3-biopython/usr/lib/python3/dist-packages/biopython-1.81.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.11')}, 'ext_no_version': set()}
D: dh_python3 depends:117: generating dependencies for package python3-biopython
D: dh_python3 pydist:173: trying to find dependency for numpy (python=None)
D: dh_python3 pydist:207: dependency: module seems to be installed
D: dh_python3 pydist:270: dependency: included in build-deps
D: dh_python3 depends:281: D={'python3-numpy', 'python3 (>= 3.11~)', 'python3:any', 'python3 (<< 3.12)'}; R=[]; S=[]; E=[], B=[]; RT=[]
   dh_installsystemduser -a -O--buildsystem=pybuild
   dh_lintian -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/usr/share/lintian/overrides
	install -p -m0644 debian/python3-biopython.lintian-overrides debian/python3-biopython/usr/share/lintian/overrides/python3-biopython
   dh_perl -a -O--buildsystem=pybuild
   dh_link -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs
	rm -f debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd
	ln -s ../../../../../../share/xml/w3c-sgml-lib/schema/dtd/XX-MathML2-20031104/mathml2.dtd debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd
   dh_strip_nondeterminism -a -O--buildsystem=pybuild
   dh_compress -a -O--buildsystem=pybuild
	cd debian/python3-biopython
	chmod a-x usr/share/doc/python3-biopython/CONTRIB.rst usr/share/doc/python3-biopython/DEPRECATED.rst usr/share/doc/python3-biopython/NEWS.Debian usr/share/doc/python3-biopython/NEWS.rst usr/share/doc/python3-biopython/changelog.Debian
	gzip -9nf usr/share/doc/python3-biopython/CONTRIB.rst usr/share/doc/python3-biopython/DEPRECATED.rst usr/share/doc/python3-biopython/NEWS.Debian usr/share/doc/python3-biopython/NEWS.rst usr/share/doc/python3-biopython/changelog.Debian
	cd '/<<PKGBUILDDIR>>'
	rm -f debian/python3-biopython.debhelper.log
   debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
	find debian/python3-biopython ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/python3-biopython/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-biopython/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python3-biopython/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/python3-biopython/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python3-biopython -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python3-biopython/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian -name "*.dtd" -exec chmod -x \{\} \;
chmod: cannot operate on dangling symlink 'debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_missing -a -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/usr/lib/debug/.dwz/arm-linux-gnueabihf
	dwz -mdebian/python3-biopython/usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-biopython.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-biopython.debug -- debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so
	objcopy --compress-debug-sections debian/python3-biopython/usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-biopython.debug
	chmod 0644 -- debian/python3-biopython/usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-biopython.debug
   dh_strip -a -O--buildsystem=pybuild
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/e0
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/e0/802abbe0dde529ceffa612f88ac55886df3df7.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/e0/802abbe0dde529ceffa612f88ac55886df3df7.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/e0/802abbe0dde529ceffa612f88ac55886df3df7.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/83
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/83/8cbf9186c8474f49aeda09a8dcf05b3be4aaf6.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/83/8cbf9186c8474f49aeda09a8dcf05b3be4aaf6.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/83/8cbf9186c8474f49aeda09a8dcf05b3be4aaf6.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/0c
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/0c/24f307a3c43179652157b991883a386396bd95.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/0c/24f307a3c43179652157b991883a386396bd95.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/0c/24f307a3c43179652157b991883a386396bd95.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/b3
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/b3/c4d44f91273b5a2aabe26dd149cd10cc033b76.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/b3/c4d44f91273b5a2aabe26dd149cd10cc033b76.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/b3/c4d44f91273b5a2aabe26dd149cd10cc033b76.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/61
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/61/eddd826cc089ea4c9ca3d11753ece4c5a008fa.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/61/eddd826cc089ea4c9ca3d11753ece4c5a008fa.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/61/eddd826cc089ea4c9ca3d11753ece4c5a008fa.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/c3
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/c3/7443d2e2fd3f60f887c602facf007d62669e55.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/c3/7443d2e2fd3f60f887c602facf007d62669e55.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/c3/7443d2e2fd3f60f887c602facf007d62669e55.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/86
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/86/a3ae4bc92b6899b15e9db1ddd28c775af8b7b6.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/86/a3ae4bc92b6899b15e9db1ddd28c775af8b7b6.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/86/a3ae4bc92b6899b15e9db1ddd28c775af8b7b6.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/a0
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/a0/e9eccfe31c0f024670201a59c1e73590f99429.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/a0/e9eccfe31c0f024670201a59c1e73590f99429.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/a0/e9eccfe31c0f024670201a59c1e73590f99429.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/4e
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/4e/e378c6c3b2d411e85c687c9f76b13c470a5d96.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/4e/e378c6c3b2d411e85c687c9f76b13c470a5d96.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/4e/e378c6c3b2d411e85c687c9f76b13c470a5d96.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.dwz
	cp --reflink=auto -a debian/python3-biopython/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.dwz
	rm -fr debian/python3-biopython/usr/lib/debug/.dwz
	rmdir -p --ignore-fail-on-non-empty debian/python3-biopython/usr/lib/debug
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/usr/share/doc
	ln -s python3-biopython debian/.debhelper/python3-biopython/dbgsym-root/usr/share/doc/python3-biopython-dbgsym
	install -m0755 -d debian/.debhelper/python3-biopython
   dh_makeshlibs -a -O--buildsystem=pybuild
	rm -f debian/python3-biopython/DEBIAN/shlibs
   dh_shlibdeps -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/DEBIAN
	dpkg-shlibdeps -Tdebian/python3-biopython.substvars debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so
   dh_installdeb -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/DEBIAN
	printf '#!/bin/sh\nset -e\n' > debian/python3-biopython/DEBIAN/postinst
	cat debian/python3-biopython.postinst.debhelper >> debian/python3-biopython/DEBIAN/postinst
	chmod 0755 -- debian/python3-biopython/DEBIAN/postinst
	printf '#!/bin/sh\nset -e\n' > debian/python3-biopython/DEBIAN/prerm
	cat debian/python3-biopython.prerm.debhelper >> debian/python3-biopython/DEBIAN/prerm
	chmod 0755 -- debian/python3-biopython/DEBIAN/prerm
   dh_gencontrol -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/DEBIAN
	echo misc:Depends= >> debian/python3-biopython.substvars
	echo misc:Pre-Depends= >> debian/python3-biopython.substvars
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN
	dpkg-gencontrol -ppython3-biopython -ldebian/changelog -Tdebian/python3-biopython.substvars -Pdebian/.debhelper/python3-biopython/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=python3-biopython-dbgsym "-DDepends=python3-biopython (= \${binary:Version})" "-DDescription=debug symbols for python3-biopython" "-DBuild-Ids=0c24f307a3c43179652157b991883a386396bd95 4ee378c6c3b2d411e85c687c9f76b13c470a5d96 61eddd826cc089ea4c9ca3d11753ece4c5a008fa 838cbf9186c8474f49aeda09a8dcf05b3be4aaf6 86a3ae4bc92b6899b15e9db1ddd28c775af8b7b6 a0e9eccfe31c0f024670201a59c1e73590f99429 b3c4d44f91273b5a2aabe26dd149cd10cc033b76 c37443d2e2fd3f60f887c602facf007d62669e55 e0802abbe0dde529ceffa612f88ac55886df3df7" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -ppython3-biopython -ldebian/changelog -Tdebian/python3-biopython.substvars -Pdebian/python3-biopython
	chmod 0644 -- debian/python3-biopython/DEBIAN/control
   dh_md5sums -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-biopython/DEBIAN
	cd debian/python3-biopython >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/python3-biopython/DEBIAN/md5sums
	install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN
	cd debian/.debhelper/python3-biopython/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN/md5sums
   dh_builddeb -a -O--buildsystem=pybuild
	dpkg-deb --root-owner-group --build debian/python3-biopython ..
	dpkg-deb --root-owner-group --build debian/.debhelper/python3-biopython/dbgsym-root ..
dpkg-deb: building package 'python3-biopython-dbgsym' in '../python3-biopython-dbgsym_1.81+dfsg-2_armhf.deb'.
dpkg-deb: building package 'python3-biopython' in '../python3-biopython_1.81+dfsg-2_armhf.deb'.
 dpkg-genbuildinfo --build=any -O../python-biopython_1.81+dfsg-2_armhf.buildinfo
 dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../python-biopython_1.81+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-11-14T07:12:19Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


python-biopython_1.81+dfsg-2_armhf.changes:
-------------------------------------------

Format: 1.8
Date: Sat, 11 Nov 2023 11:16:46 +0100
Source: python-biopython
Binary: python3-biopython python3-biopython-dbgsym
Architecture: armhf
Version: 1.81+dfsg-2
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
 python3-biopython - Python3 library for bioinformatics
Closes: 1055708
Changes:
 python-biopython (1.81+dfsg-2) unstable; urgency=medium
 .
   * python3.12.patch: new: fix ftbfs with python3.12.
     Thanks to Antonio (Closes: #1055708)
   * d/control: remove obsolete comment.
   * d/control: move to dh-sequence-python3.
Checksums-Sha1:
 d99580ef6407966951808649e4e13b772e0582e6 12848 python-biopython_1.81+dfsg-2_armhf.buildinfo
 42e673892e435184ad20e045116f4854d0de8f7a 292284 python3-biopython-dbgsym_1.81+dfsg-2_armhf.deb
 42222800c35c4fc437b19620e37455827b43a6f8 1570240 python3-biopython_1.81+dfsg-2_armhf.deb
Checksums-Sha256:
 5dece57268e0977d13bb5fe397a8ee8b02c847039d88e3d85c20ac2e0e6c65ca 12848 python-biopython_1.81+dfsg-2_armhf.buildinfo
 13c67fbe2d6a77acd8d9330fb1031e96df9da7460bdf1d49e7606397de675562 292284 python3-biopython-dbgsym_1.81+dfsg-2_armhf.deb
 ca8433719046a1483180cf664ce8f3d76e88e0cd5f2d127a841227248295475f 1570240 python3-biopython_1.81+dfsg-2_armhf.deb
Files:
 b11e3e4eaeea590be02c522c37533189 12848 python optional python-biopython_1.81+dfsg-2_armhf.buildinfo
 a31952ebd099e8b3294952fc0b5dddd6 292284 debug optional python3-biopython-dbgsym_1.81+dfsg-2_armhf.deb
 47e67137221544ce2d9b3c2114bde771 1570240 python optional python3-biopython_1.81+dfsg-2_armhf.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: python-biopython
Binary: python3-biopython python3-biopython-dbgsym
Architecture: armhf
Version: 1.81+dfsg-2
Checksums-Md5:
 a31952ebd099e8b3294952fc0b5dddd6 292284 python3-biopython-dbgsym_1.81+dfsg-2_armhf.deb
 47e67137221544ce2d9b3c2114bde771 1570240 python3-biopython_1.81+dfsg-2_armhf.deb
Checksums-Sha1:
 42e673892e435184ad20e045116f4854d0de8f7a 292284 python3-biopython-dbgsym_1.81+dfsg-2_armhf.deb
 42222800c35c4fc437b19620e37455827b43a6f8 1570240 python3-biopython_1.81+dfsg-2_armhf.deb
Checksums-Sha256:
 13c67fbe2d6a77acd8d9330fb1031e96df9da7460bdf1d49e7606397de675562 292284 python3-biopython-dbgsym_1.81+dfsg-2_armhf.deb
 ca8433719046a1483180cf664ce8f3d76e88e0cd5f2d127a841227248295475f 1570240 python3-biopython_1.81+dfsg-2_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 14 Nov 2023 07:12:18 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.71-3),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.21-13),
 autotools-dev (= 20220109.1),
 base-files (= 13+rpi1),
 base-passwd (= 3.6.2),
 bash (= 5.2.15-2),
 binutils (= 2.41-6+rpi1),
 binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
 binutils-common (= 2.41-6+rpi1),
 blt (= 2.5.3+dfsg-4.1),
 bsdextrautils (= 2.39.2-5),
 bsdutils (= 1:2.39.2-5),
 build-essential (= 12.9),
 bwa (= 0.7.17-7),
 bzip2 (= 1.0.8-5+b2),
 clustalo (= 1.2.4-7),
 clustalw (= 2.1+lgpl-7),
 coreutils (= 9.1-1),
 cpp (= 4:13.2.0-1+rpi1),
 cpp-12 (= 12.3.0-10+rpi1),
 cpp-13 (= 13.2.0-5+rpi1),
 dash (= 0.5.12-6),
 debconf (= 1.5.82),
 debhelper (= 13.11.7),
 debianutils (= 5.14),
 dh-autoreconf (= 20),
 dh-python (= 6.20231107),
 dh-strip-nondeterminism (= 1.13.1-1),
 dialign (= 2.2.1-11),
 diffutils (= 1:3.10-1),
 dpkg (= 1.22.1+rpi1),
 dpkg-dev (= 1.22.1+rpi1),
 dssp (= 4.2.2-2),
 dwz (= 0.15-1),
 emboss (= 6.6.0+dfsg-12),
 emboss-data (= 6.6.0+dfsg-12),
 emboss-lib (= 6.6.0+dfsg-12),
 fasttree (= 2.1.11-2),
 file (= 1:5.45-2),
 findutils (= 4.9.0-5),
 flex (= 2.6.4-8.2),
 fontconfig-config (= 2.14.2-6),
 fonts-dejavu-core (= 2.37-8),
 fonts-dejavu-extra (= 2.37-8),
 fonts-dejavu-mono (= 2.37-8),
 fonts-lmodern (= 2.005-1),
 fonts-lyx (= 2.3.7-1),
 fonts-urw-base35 (= 20200910-7),
 g++ (= 4:13.2.0-1+rpi1),
 g++-13 (= 13.2.0-5+rpi1),
 gcc (= 4:13.2.0-1+rpi1),
 gcc-12 (= 12.3.0-10+rpi1),
 gcc-12-base (= 12.3.0-10+rpi1),
 gcc-13 (= 13.2.0-5+rpi1),
 gcc-13-base (= 13.2.0-5+rpi1),
 gettext (= 0.21-13),
 gettext-base (= 0.21-13),
 ghostscript (= 10.02.0~dfsg-2),
 grep (= 3.11-3),
 groff-base (= 1.23.0-3),
 gzip (= 1.12-1),
 hevea (= 2.36-2),
 hicolor-icon-theme (= 0.17-2),
 hostname (= 3.23+nmu1),
 imagemagick (= 8:6.9.12.98+dfsg1-3),
 imagemagick-6-common (= 8:6.9.12.98+dfsg1-3),
 imagemagick-6.q16 (= 8:6.9.12.98+dfsg1-3),
 init-system-helpers (= 1.65.2),
 intltool-debian (= 0.35.0+20060710.6),
 libabsl20220623 (= 20220623.1-3),
 libacl1 (= 2.3.1-3),
 libaom3 (= 3.7.0-1),
 libapache-pom-java (= 29-2),
 libarchive-zip-perl (= 1.68-1),
 libargtable2-0 (= 13-1.1),
 libasan8 (= 13.2.0-5+rpi1),
 libatomic1 (= 13.2.0-5+rpi1),
 libattr1 (= 1:2.5.1-4),
 libaudit-common (= 1:3.1.1-1),
 libaudit1 (= 1:3.1.1-1),
 libavahi-client3 (= 0.8-13),
 libavahi-common-data (= 0.8-13),
 libavahi-common3 (= 0.8-13),
 libavif16 (= 1.0.1-2),
 libbinutils (= 2.41-6+rpi1),
 libblas3 (= 3.11.0-2),
 libblkid1 (= 2.39.2-5),
 libboost-regex1.74.0 (= 1.74.0+ds1-23),
 libbrotli1 (= 1.0.9-2+b3),
 libbsd0 (= 0.11.7-4),
 libbz2-1.0 (= 1.0.8-5+b2),
 libc-bin (= 2.37-12+rpi2),
 libc-dev-bin (= 2.37-12+rpi2),
 libc6 (= 2.37-12+rpi2),
 libc6-dev (= 2.37-12+rpi2),
 libcairo2 (= 1.18.0-1),
 libcap-ng0 (= 0.8.3-1+b1),
 libcap2 (= 1:2.66-4),
 libcc1-0 (= 13.2.0-5+rpi1),
 libcifpp-data (= 5.0.7.1-3),
 libcifpp5 (= 5.0.7.1-3),
 libcom-err2 (= 1.47.0-2),
 libcommons-logging-java (= 1.2-4),
 libcommons-parent-java (= 56-1),
 libcrypt-dev (= 1:4.4.36-2),
 libcrypt1 (= 1:4.4.36-2),
 libctf-nobfd0 (= 2.41-6+rpi1),
 libctf0 (= 2.41-6+rpi1),
 libcups2 (= 2.4.7-1),
 libcurl3-gnutls (= 8.4.0-2+rpi1),
 libdav1d6 (= 1.2.1-2+rpi1),
 libdb5.3 (= 5.3.28+dfsg2-2),
 libdbus-1-3 (= 1.14.10-3),
 libde265-0 (= 1.0.11-1+rpi1+b1),
 libdebconfclient0 (= 0.271),
 libdebhelper-perl (= 13.11.7),
 libdeflate0 (= 1.18-1),
 libdpkg-perl (= 1.22.1+rpi1),
 libelf1 (= 0.188-2.1+rpi1),
 libexpat1 (= 2.5.0-2),
 libexpat1-dev (= 2.5.0-2),
 libffi8 (= 3.4.4-1),
 libfftw3-double3 (= 3.3.10-1),
 libfile-stripnondeterminism-perl (= 1.13.1-1),
 libfontbox-java (= 1:1.8.16-4),
 libfontconfig1 (= 2.14.2-6),
 libfontenc1 (= 1:1.1.4-1),
 libfreetype6 (= 2.13.2+dfsg-1),
 libfribidi0 (= 1.0.13-3),
 libgav1-1 (= 0.18.0-1+rpi1+b1),
 libgcc-12-dev (= 12.3.0-10+rpi1),
 libgcc-13-dev (= 13.2.0-5+rpi1),
 libgcc-s1 (= 13.2.0-5+rpi1),
 libgcrypt20 (= 1.10.2-3),
 libgd3 (= 2.3.3-9+b1),
 libgdbm-compat4 (= 1.23-3),
 libgdbm6 (= 1.23-3),
 libgfortran5 (= 13.2.0-5+rpi1),
 libglib2.0-0 (= 2.78.1-2),
 libgmp10 (= 2:6.3.0+dfsg-2),
 libgnutls30 (= 3.8.1-4),
 libgomp1 (= 13.2.0-5+rpi1),
 libgpg-error0 (= 1.47-2),
 libgraphite2-3 (= 1.3.14-1),
 libgs-common (= 10.02.0~dfsg-2),
 libgs10 (= 10.02.0~dfsg-2),
 libgs10-common (= 10.02.0~dfsg-2),
 libgssapi-krb5-2 (= 1.20.1-4),
 libharfbuzz0b (= 8.0.1-1),
 libheif-plugin-dav1d (= 1.17.1-1),
 libheif-plugin-libde265 (= 1.17.1-1),
 libheif1 (= 1.17.1-1),
 libhogweed6 (= 3.9.1-2),
 libhpdf-2.3.0 (= 2.3.0+dfsg-1),
 libhts3 (= 1.18+ds-1),
 libhtscodecs2 (= 1.5.2-1),
 libice6 (= 2:1.0.10-1),
 libicu72 (= 72.1-4),
 libidn12 (= 1.41-1+b1),
 libidn2-0 (= 2.3.4-1),
 libijs-0.35 (= 0.35-15.1),
 libimagequant0 (= 2.17.0-1),
 libisl23 (= 0.26-3),
 libjansson4 (= 2.14-2),
 libjbig0 (= 2.1-6.1),
 libjbig2dec0 (= 0.19-3+b2),
 libjpeg62-turbo (= 1:2.1.5-2),
 libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
 libjs-jquery-ui (= 1.13.2+dfsg-1),
 libjs-sphinxdoc (= 7.2.6-2),
 libjs-underscore (= 1.13.4~dfsg+~1.11.4-3),
 libk5crypto3 (= 1.20.1-4),
 libkeyutils1 (= 1.6.3-2),
 libkpathsea6 (= 2023.20230311.66589-6),
 libkrb5-3 (= 1.20.1-4),
 libkrb5support0 (= 1.20.1-4),
 liblapack3 (= 3.11.0-2),
 liblbfgsb0 (= 3.0+dfsg.4-1),
 liblcms2-2 (= 2.14-2),
 libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
 liblerc4 (= 4.0.0+ds-3),
 liblmdb0 (= 0.9.31-1),
 liblqr-1-0 (= 0.4.2-2.1),
 libltdl7 (= 2.4.7-7),
 liblz4-1 (= 1.9.4-1+rpi1+b1),
 liblzma5 (= 5.4.4-0.1),
 libmagic-mgc (= 1:5.45-2),
 libmagic1 (= 1:5.45-2),
 libmagickcore-6.q16-7 (= 8:6.9.12.98+dfsg1-3),
 libmagickwand-6.q16-7 (= 8:6.9.12.98+dfsg1-3),
 libmariadb3 (= 1:10.11.3-1+rpi1),
 libmbedcrypto7 (= 2.28.5-1),
 libmbedtls14 (= 2.28.5-1),
 libmbedx509-1 (= 2.28.5-1),
 libmd0 (= 1.1.0-1),
 libmount1 (= 2.39.2-5),
 libmpc3 (= 1.3.1-1),
 libmpfr6 (= 4.2.1-1),
 libncurses6 (= 6.4+20231016-1),
 libncursesw6 (= 6.4+20231016-1),
 libnetpbm11 (= 2:11.03.06-1),
 libnettle8 (= 3.9.1-2),
 libnghttp2-14 (= 1.58.0-1),
 libnsl-dev (= 1.3.0-2),
 libnsl2 (= 1.3.0-2),
 libopenjp2-7 (= 2.5.0-2),
 libp11-kit0 (= 0.25.0-5),
 libpam-modules (= 1.5.2-9.1),
 libpam-modules-bin (= 1.5.2-9.1),
 libpam-runtime (= 1.5.2-9.1),
 libpam0g (= 1.5.2-9.1),
 libpaper-utils (= 1.1.29),
 libpaper1 (= 1.1.29),
 libpcre2-8-0 (= 10.42-4),
 libpdfbox-java (= 1:1.8.16-4),
 libperl5.36 (= 5.36.0-9),
 libpipeline1 (= 1.5.7-1),
 libpixman-1-0 (= 0.42.2-1),
 libpng16-16 (= 1.6.40-2),
 libpotrace0 (= 1.16-2),
 libpq5 (= 16.0-2),
 libpsl5 (= 0.21.2-1+b1),
 libptexenc1 (= 2023.20230311.66589-6),
 libpython3-all-dev (= 3.11.4-5),
 libpython3-dev (= 3.11.4-5),
 libpython3-stdlib (= 3.11.4-5),
 libpython3.11 (= 3.11.6-3),
 libpython3.11-dev (= 3.11.6-3),
 libpython3.11-minimal (= 3.11.6-3),
 libpython3.11-stdlib (= 3.11.6-3),
 libqhull-r8.0 (= 2020.2-6),
 libraqm0 (= 0.10.1-1),
 librav1e0 (= 0.6.6-3+rpi1),
 libraw23 (= 0.21.1-7+rpi1),
 libreadline8 (= 8.2-1.3),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
 libsasl2-2 (= 2.1.28+dfsg1-3),
 libsasl2-modules-db (= 2.1.28+dfsg1-3),
 libseccomp2 (= 2.5.4-1+rpi1+b1),
 libselinux1 (= 3.5-1),
 libsframe1 (= 2.41-6+rpi1),
 libsharpyuv0 (= 1.3.2-0.3),
 libsm6 (= 2:1.2.3-1),
 libsmartcols1 (= 2.39.2-5),
 libsqlite3-0 (= 3.43.2-1),
 libssh2-1 (= 1.11.0-2),
 libssl3 (= 3.0.11-1),
 libstdc++-13-dev (= 13.2.0-5+rpi1),
 libstdc++6 (= 13.2.0-5+rpi1),
 libsub-override-perl (= 0.09-4),
 libsvtav1enc1d1 (= 1.7.0+dfsg-2),
 libsynctex2 (= 2023.20230311.66589-6),
 libsystemd0 (= 254.5-1+rpi1),
 libtasn1-6 (= 4.19.0-3),
 libtcl8.6 (= 8.6.13+dfsg-2),
 libteckit0 (= 2.5.11+ds1-1),
 libtexlua53-5 (= 2023.20230311.66589-6),
 libtiff6 (= 4.5.1+git230720-1),
 libtinfo6 (= 6.4+20231016-1),
 libtirpc-common (= 1.3.3+ds-1),
 libtirpc-dev (= 1.3.3+ds-1),
 libtirpc3 (= 1.3.3+ds-1),
 libtk8.6 (= 8.6.13-2),
 libtool (= 2.4.7-7),
 libubsan1 (= 13.2.0-5+rpi1),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 254.5-1+rpi1),
 libunistring5 (= 1.1-2),
 libuuid1 (= 2.39.2-5),
 libwebp7 (= 1.3.2-0.3),
 libwebpdemux2 (= 1.3.2-0.3),
 libwebpmux3 (= 1.3.2-0.3),
 libx11-6 (= 2:1.8.7-1),
 libx11-data (= 2:1.8.7-1),
 libxau6 (= 1:1.0.9-1),
 libxaw7 (= 2:1.0.14-1),
 libxcb-render0 (= 1.15-1),
 libxcb-shm0 (= 1.15-1),
 libxcb1 (= 1.15-1),
 libxdmcp6 (= 1:1.1.2-3),
 libxext6 (= 2:1.3.4-1),
 libxft2 (= 2.3.6-1),
 libxi6 (= 2:1.8-1),
 libxml2 (= 2.9.14+dfsg-1.3),
 libxmu6 (= 2:1.1.3-3),
 libxpm4 (= 1:3.5.17-1),
 libxrender1 (= 1:0.9.10-1.1),
 libxslt1.1 (= 1.1.35-1),
 libxss1 (= 1:1.2.3-1),
 libxt6 (= 1:1.2.1-1.1),
 libyuv0 (= 0.0~git20230907.cbfb661-1),
 libzstd1 (= 1.5.5+dfsg2-2),
 libzzip-0-13 (= 0.13.72+dfsg.1-1.1),
 linux-libc-dev (= 6.5.6-1+rpi1),
 login (= 1:4.13+dfsg1-3),
 lsb-base (= 11.6+rpi1),
 m4 (= 1.4.19-4),
 mafft (= 7.505-1),
 mailcap (= 3.70+nmu1),
 make (= 4.3-4.1),
 man-db (= 2.12.0-1),
 mariadb-common (= 1:10.11.3-1+rpi1),
 mawk (= 1.3.4.20230808-1),
 media-types (= 10.1.0),
 mime-support (= 3.66),
 mysql-common (= 5.8+1.1.0),
 ncbi-blast+ (= 2.12.0+ds-4),
 ncbi-data (= 6.1.20170106+dfsg1-10),
 ncurses-base (= 6.4+20231016-1),
 ncurses-bin (= 6.4+20231016-1),
 netpbm (= 2:11.03.06-1),
 patch (= 2.7.6-7),
 perl (= 5.36.0-9),
 perl-base (= 5.36.0-9),
 perl-modules-5.36 (= 5.36.0-9),
 phylip (= 1:3.697+dfsg-2),
 po-debconf (= 1.0.21+nmu1),
 poppler-data (= 0.4.12-1),
 prank (= 0.0.170427+dfsg-3),
 preview-latex-style (= 12.2-1),
 probcons (= 1.12-14),
 python-matplotlib-data (= 3.6.3-1),
 python3 (= 3.11.4-5),
 python3-all (= 3.11.4-5),
 python3-all-dev (= 3.11.4-5),
 python3-appdirs (= 1.4.4-4),
 python3-attr (= 23.1.0-2),
 python3-brotli (= 1.0.9-2+b3),
 python3-cairo (= 1.24.0-3),
 python3-contourpy (= 1.0.7-1),
 python3-cycler (= 0.11.0-1),
 python3-dateutil (= 2.8.2-3),
 python3-decorator (= 5.1.1-5),
 python3-dev (= 3.11.4-5),
 python3-distutils (= 3.11.5-1),
 python3-fonttools (= 4.38.0-1),
 python3-freetype (= 2.4.0-1),
 python3-fs (= 2.4.16-2),
 python3-isodate (= 0.6.1-1),
 python3-kiwisolver (= 1.4.4-1),
 python3-lib2to3 (= 3.11.5-1),
 python3-lxml (= 4.9.3-1),
 python3-lz4 (= 4.0.2+dfsg-1+b1),
 python3-matplotlib (= 3.6.3-1),
 python3-minimal (= 3.11.4-5),
 python3-mmtf (= 1.1.3-1),
 python3-mpmath (= 1.2.1-2),
 python3-msgpack (= 1.0.3-3),
 python3-mysqldb (= 1.4.6-2+b1),
 python3-networkx (= 2.8.8-1),
 python3-numpy (= 1:1.24.2-1),
 python3-packaging (= 23.1-1),
 python3-pil (= 10.0.0-1),
 python3-pil.imagetk (= 10.0.0-1),
 python3-pkg-resources (= 68.1.2-2),
 python3-psycopg2 (= 2.9.6-3),
 python3-pygments (= 2.15.1+dfsg-1),
 python3-pyparsing (= 3.1.1-1),
 python3-rdflib (= 6.1.1-2),
 python3-reportlab (= 4.0.4-11),
 python3-rlpycairo (= 0.3.0-3),
 python3-scipy (= 1.10.1-2+rpi1),
 python3-setuptools (= 68.1.2-2),
 python3-six (= 1.16.0-4),
 python3-sympy (= 1.12-6),
 python3-tk (= 3.11.5-1),
 python3-tz (= 2023.3.post1-1),
 python3-ufolib2 (= 0.16.0+dfsg1-1),
 python3-unittest2 (= 1.1.0-9),
 python3.11 (= 3.11.6-3),
 python3.11-dev (= 3.11.6-3),
 python3.11-minimal (= 3.11.6-3),
 readline-common (= 8.2-1.3),
 rpcsvc-proto (= 1.4.3-1),
 samtools (= 1.18-1),
 sed (= 4.9-1),
 sensible-utils (= 0.0.20),
 sysvinit-utils (= 3.08-3),
 t-coffee (= 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1),
 t1utils (= 1.41-4),
 tar (= 1.34+dfsg-1.2),
 tex-common (= 6.18),
 texlive-base (= 2023.20231007-1),
 texlive-binaries (= 2023.20230311.66589-6),
 texlive-fonts-recommended (= 2023.20231007-1),
 texlive-latex-base (= 2023.20231007-1),
 texlive-latex-extra (= 2023.20231007-2),
 texlive-latex-recommended (= 2023.20231007-1),
 texlive-pictures (= 2023.20231007-1),
 tk8.6-blt2.5 (= 2.5.3+dfsg-4.1),
 tzdata (= 2023c-10),
 ucf (= 3.0043+nmu1),
 unicode-data (= 15.1.0-1),
 usr-is-merged (= 37),
 util-linux (= 2.39.2-5),
 wise (= 2.4.1-23),
 wise-data (= 2.4.1-23),
 x11-common (= 1:7.7+23),
 xdg-utils (= 1.1.3-4.1),
 xfonts-encodings (= 1:1.0.4-2.2),
 xfonts-utils (= 1:7.7+6),
 xz-utils (= 5.4.4-0.1),
 zlib1g (= 1:1.2.13.dfsg-3),
 zlib1g-dev (= 1:1.2.13.dfsg-3)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 SOURCE_DATE_EPOCH="1699697806"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


python3-biopython-dbgsym_1.81+dfsg-2_armhf.deb
----------------------------------------------

 new Debian package, version 2.0.
 size 292284 bytes: control archive=1004 bytes.
     745 bytes,    12 lines      control
    1051 bytes,    10 lines      md5sums
 Package: python3-biopython-dbgsym
 Source: python-biopython
 Version: 1.81+dfsg-2
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 364
 Depends: python3-biopython (= 1.81+dfsg-2)
 Section: debug
 Priority: optional
 Description: debug symbols for python3-biopython
 Build-Ids: 0c24f307a3c43179652157b991883a386396bd95 4ee378c6c3b2d411e85c687c9f76b13c470a5d96 61eddd826cc089ea4c9ca3d11753ece4c5a008fa 838cbf9186c8474f49aeda09a8dcf05b3be4aaf6 86a3ae4bc92b6899b15e9db1ddd28c775af8b7b6 a0e9eccfe31c0f024670201a59c1e73590f99429 b3c4d44f91273b5a2aabe26dd149cd10cc033b76 c37443d2e2fd3f60f887c602facf007d62669e55 e0802abbe0dde529ceffa612f88ac55886df3df7

drwxr-xr-x root/root         0 2023-11-11 10:16 ./
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root     92828 2023-11-11 10:16 ./usr/lib/debug/.build-id/0c/24f307a3c43179652157b991883a386396bd95.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/4e/
-rw-r--r-- root/root     10116 2023-11-11 10:16 ./usr/lib/debug/.build-id/4e/e378c6c3b2d411e85c687c9f76b13c470a5d96.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/61/
-rw-r--r-- root/root     28472 2023-11-11 10:16 ./usr/lib/debug/.build-id/61/eddd826cc089ea4c9ca3d11753ece4c5a008fa.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/83/
-rw-r--r-- root/root    156796 2023-11-11 10:16 ./usr/lib/debug/.build-id/83/8cbf9186c8474f49aeda09a8dcf05b3be4aaf6.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/86/
-rw-r--r-- root/root      7464 2023-11-11 10:16 ./usr/lib/debug/.build-id/86/a3ae4bc92b6899b15e9db1ddd28c775af8b7b6.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/a0/
-rw-r--r-- root/root      6160 2023-11-11 10:16 ./usr/lib/debug/.build-id/a0/e9eccfe31c0f024670201a59c1e73590f99429.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/b3/
-rw-r--r-- root/root     13592 2023-11-11 10:16 ./usr/lib/debug/.build-id/b3/c4d44f91273b5a2aabe26dd149cd10cc033b76.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/c3/
-rw-r--r-- root/root      9416 2023-11-11 10:16 ./usr/lib/debug/.build-id/c3/7443d2e2fd3f60f887c602facf007d62669e55.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.build-id/e0/
-rw-r--r-- root/root     14848 2023-11-11 10:16 ./usr/lib/debug/.build-id/e0/802abbe0dde529ceffa612f88ac55886df3df7.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root      6260 2023-11-11 10:16 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-biopython.debug
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/share/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/share/doc/
lrwxrwxrwx root/root         0 2023-11-11 10:16 ./usr/share/doc/python3-biopython-dbgsym -> python3-biopython


python3-biopython_1.81+dfsg-2_armhf.deb
---------------------------------------

 new Debian package, version 2.0.
 size 1570240 bytes: control archive=17820 bytes.
    1453 bytes,    26 lines      control
   63969 bytes,   677 lines      md5sums
     281 bytes,    12 lines   *  postinst             #!/bin/sh
     394 bytes,    12 lines   *  prerm                #!/bin/sh
 Package: python3-biopython
 Source: python-biopython
 Version: 1.81+dfsg-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 11242
 Depends: python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3 (<< 3.12), python3 (>= 3.11~), python3:any, libc6 (>= 2.4), python3-reportlab (>= 4.0.4-1~), w3c-sgml-lib
 Recommends: python-biopython-doc (= 1.81+dfsg-2), ncbi-blast+ (>= 2.10.1-3)
 Suggests: python3-tk, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle3, phylip, phyml, prank, probcons, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-scipy, raxml, samtools, t-coffee, wise
 Breaks: ncbi-acc-download (<< 0.2.7-2~)
 Section: python
 Priority: optional
 Homepage: https://biopython.org
 Description: Python3 library for bioinformatics
  The Biopython Project is an international association
  of developers of freely available Python tools for
  computational molecular biology.
  .
  It is a distributed collaborative effort to develop Python3
  libraries and applications which address the needs of
  current and future work in bioinformatics. The source code
  is made available under the Biopython License, which is
  extremely liberal and compatible with almost every license in
  the world. The project works along with the Open Bioinformatics
  Foundation, who generously provide web and CVS space for
  the project.

drwxr-xr-x root/root         0 2023-11-11 10:16 ./
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Affy/
-rw-r--r-- root/root     23670 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Affy/CelFile.py
-rw-r--r-- root/root       296 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Affy/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Align/
-rw-r--r-- root/root     22468 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/AlignInfo.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Align/Applications/
-rw-r--r-- root/root     10012 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_ClustalOmega.py
-rw-r--r-- root/root     20228 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Clustalw.py
-rw-r--r-- root/root     10101 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Dialign.py
-rw-r--r-- root/root      3444 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_MSAProbs.py
-rw-r--r-- root/root     19884 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Mafft.py
-rw-r--r-- root/root     36013 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Muscle.py
-rw-r--r-- root/root     10544 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Prank.py
-rw-r--r-- root/root      5238 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Probcons.py
-rw-r--r-- root/root      4588 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_TCoffee.py
-rw-r--r-- root/root      1193 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/Applications/__init__.py
-rw-r--r-- root/root    139236 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/__init__.py
-rw-r--r-- root/root    235898 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/_aligners.c
-rw-r--r-- root/root    123244 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so
-rw-r--r-- root/root      4531 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/a2m.py
-rw-r--r-- root/root      9271 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/bed.py
-rw-r--r-- root/root     26541 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/bigbed.py
-rw-r--r-- root/root      1834 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/bigmaf.py
-rw-r--r-- root/root      7948 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/bigpsl.py
-rw-r--r-- root/root      9413 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/clustal.py
-rw-r--r-- root/root     10247 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/emboss.py
-rw-r--r-- root/root     25376 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/exonerate.py
-rw-r--r-- root/root      3080 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/fasta.py
-rw-r--r-- root/root      9503 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/hhr.py
-rw-r--r-- root/root      8518 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/interfaces.py
-rw-r--r-- root/root     18265 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/maf.py
-rw-r--r-- root/root      9818 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/mauve.py
-rw-r--r-- root/root      9350 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/msf.py
-rw-r--r-- root/root      7236 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/nexus.py
-rw-r--r-- root/root      6441 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/phylip.py
-rw-r--r-- root/root     21685 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/psl.py
-rw-r--r-- root/root     29829 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/sam.py
-rw-r--r-- root/root     25573 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/stockholm.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/
-rw-r--r-- root/root     17844 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/
-rw-r--r-- root/root      2387 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22
-rw-r--r-- root/root      2387 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6
-rw-r--r-- root/root      2387 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74
-rw-r--r-- root/root      1715 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN
-rw-r--r-- root/root      4009 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP
-rw-r--r-- root/root      2122 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45
-rw-r--r-- root/root      2122 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50
-rw-r--r-- root/root      2122 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62
-rw-r--r-- root/root      2124 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80
-rw-r--r-- root/root      2122 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90
-rw-r--r-- root/root      2451 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF
-rw-r--r-- root/root      1120 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG
-rw-r--r-- root/root      2380 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC
-rw-r--r-- root/root      2351 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992
-rw-r--r-- root/root       275 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70
-rw-r--r-- root/root      2818 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON
-rw-r--r-- root/root      2413 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES
-rw-r--r-- root/root      1542 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN
-rw-r--r-- root/root      1092 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN
-rw-r--r-- root/root      2859 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78
-rw-r--r-- root/root      1730 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST
-rw-r--r-- root/root      1171 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4
-rw-r--r-- root/root      2068 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250
-rw-r--r-- root/root      2666 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30
-rw-r--r-- root/root      2666 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70
-rw-r--r-- root/root      1581 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO
-rw-r--r-- root/root      2456 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER
-rw-r--r-- root/root     25459 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER
-rw-r--r-- root/root      1543 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR
-rw-r--r-- root/root       402 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS
-rw-r--r-- root/root     16530 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Align/tabular.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/AlignIO/
-rw-r--r-- root/root     12151 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/ClustalIO.py
-rw-r--r-- root/root      8748 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/EmbossIO.py
-rw-r--r-- root/root     13353 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/FastaIO.py
-rw-r--r-- root/root      5624 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/Interfaces.py
-rw-r--r-- root/root     34268 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/MafIO.py
-rw-r--r-- root/root     13287 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/MauveIO.py
-rw-r--r-- root/root     14119 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/MsfIO.py
-rw-r--r-- root/root      6024 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/NexusIO.py
-rw-r--r-- root/root     17141 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/PhylipIO.py
-rw-r--r-- root/root     26397 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/StockholmIO.py
-rw-r--r-- root/root     18615 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/AlignIO/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Alphabet/
-rw-r--r-- root/root      1200 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Alphabet/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Application/
-rw-r--r-- root/root     32073 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Application/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Blast/
-rw-r--r-- root/root     67007 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Blast/Applications.py
-rw-r--r-- root/root     14043 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Blast/NCBIWWW.py
-rw-r--r-- root/root     33437 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py
-rw-r--r-- root/root      4403 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Blast/ParseBlastTable.py
-rw-r--r-- root/root     15835 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Blast/Record.py
-rw-r--r-- root/root       350 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Blast/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/CAPS/
-rw-r--r-- root/root      4121 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/CAPS/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Cluster/
-rw-r--r-- root/root     50797 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Cluster/__init__.py
-rw-r--r-- root/root     87140 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so
-rw-r--r-- root/root    169203 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Cluster/cluster.c
-rw-r--r-- root/root      4135 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Cluster/cluster.h
-rw-r--r-- root/root     77865 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Cluster/clustermodule.c
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Compass/
-rw-r--r-- root/root      6954 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Compass/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Data/
-rw-r--r-- root/root     50327 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Data/CodonTable.py
-rw-r--r-- root/root      9224 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Data/IUPACData.py
-rw-r--r-- root/root     22893 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Data/PDBData.py
-rw-r--r-- root/root     17579 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Data/SCOPData.py
-rw-r--r-- root/root       353 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Data/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Emboss/
-rw-r--r-- root/root     49096 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Emboss/Applications.py
-rw-r--r-- root/root      5593 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Emboss/Primer3.py
-rw-r--r-- root/root      2521 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Emboss/PrimerSearch.py
-rw-r--r-- root/root       355 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Emboss/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Entrez/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/
-rw-r--r-- root/root     16498 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/BITS-embedded-index2.ent
-rw-r--r-- root/root     26770 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/BITS-question-answer2.ent
-rw-r--r-- root/root       660 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_0.dtd
-rw-r--r-- root/root     33675 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd
-rw-r--r-- root/root       660 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_1.dtd
-rw-r--r-- root/root     33691 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd
-rw-r--r-- root/root       660 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_2.dtd
-rw-r--r-- root/root     36007 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd
-rw-r--r-- root/root       660 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_3.dtd
-rw-r--r-- root/root     41304 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd
-rw-r--r-- root/root       660 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_4.dtd
-rw-r--r-- root/root     41537 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd
-rw-r--r-- root/root       792 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/EMBL_General.dtd
-rw-r--r-- root/root      2871 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/EMBL_General.mod.dtd
-rw-r--r-- root/root       807 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/GenBank_General.dtd
-rw-r--r-- root/root      1743 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/GenBank_General.mod.dtd
-rw-r--r-- root/root      3500 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/HomoloGene.dtd
-rw-r--r-- root/root      6460 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/HomoloGene.mod.dtd
-rw-r--r-- root/root       671 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/INSD_INSDSeq.dtd
-rw-r--r-- root/root     14705 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd
-rw-r--r-- root/root     31246 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent
-rw-r--r-- root/root     15260 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent
-rw-r--r-- root/root     51353 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd
-rw-r--r-- root/root     20885 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent
-rw-r--r-- root/root     31272 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent
-rw-r--r-- root/root     78956 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent
-rw-r--r-- root/root     20899 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent
-rw-r--r-- root/root    128551 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent
-rw-r--r-- root/root     26909 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-backmatter1-3.ent
-rw-r--r-- root/root     35219 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-chars1-3.ent
-rw-r--r-- root/root     18691 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-common-atts1-3.ent
-rw-r--r-- root/root    237581 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-common1-3.ent
-rw-r--r-- root/root     75822 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-default-classes1-3.ent
-rw-r--r-- root/root     32971 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent
-rw-r--r-- root/root     65828 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-display1-3.ent
-rw-r--r-- root/root     50729 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-format1-3.ent
-rw-r--r-- root/root     56436 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-funding1-3.ent
-rw-r--r-- root/root     29732 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent
-rw-r--r-- root/root     30254 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-link1-3.ent
-rw-r--r-- root/root     32721 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-list1-3.ent
-rw-r--r-- root/root     27873 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-math1-3.ent
-rw-r--r-- root/root     23901 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent
-rw-r--r-- root/root     16430 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent
-rw-r--r-- root/root     37192 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-modules1-3.ent
-rw-r--r-- root/root     21564 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent
-rw-r--r-- root/root     20223 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-notat1-3.ent
-rw-r--r-- root/root     32349 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-para1-3.ent
-rw-r--r-- root/root     33583 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-phrase1-3.ent
-rw-r--r-- root/root     73018 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-references1-3.ent
-rw-r--r-- root/root     21380 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-related-object1-3.ent
-rw-r--r-- root/root     23664 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-section1-3.ent
-rw-r--r-- root/root     24007 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent
-rw-r--r-- root/root      3893 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB.dtd
-rw-r--r-- root/root      9382 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB.mod.dtd
-rw-r--r-- root/root      3908 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd
-rw-r--r-- root/root     17213 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd
-rw-r--r-- root/root      3902 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Features.dtd
-rw-r--r-- root/root     28680 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Features.mod.dtd
-rw-r--r-- root/root      3910 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Structural_model.dtd
-rw-r--r-- root/root     25075 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd
-rw-r--r-- root/root       665 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Access.dtd
-rw-r--r-- root/root      1221 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Access.mod.dtd
-rw-r--r-- root/root       785 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Biblio.dtd
-rw-r--r-- root/root     15918 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd
-rw-r--r-- root/root       925 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioSource.dtd
-rw-r--r-- root/root      4641 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd
-rw-r--r-- root/root       671 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioTree.dtd
-rw-r--r-- root/root      2444 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd
-rw-r--r-- root/root      3740 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Blast4.dtd
-rw-r--r-- root/root     39597 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd
-rw-r--r-- root/root      3507 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastDL.dtd
-rw-r--r-- root/root      4281 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd
-rw-r--r-- root/root       692 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd
-rw-r--r-- root/root      6579 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd
-rw-r--r-- root/root      4347 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cdd.dtd
-rw-r--r-- root/root     28292 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd
-rw-r--r-- root/root      4005 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cn3d.dtd
-rw-r--r-- root/root     16758 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd
-rw-r--r-- root/root       410 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd
-rw-r--r-- root/root       671 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrez2.dtd
-rw-r--r-- root/root     21922 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd
-rw-r--r-- root/root      3525 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd
-rw-r--r-- root/root     10316 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd
-rw-r--r-- root/root       671 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_FeatDef.dtd
-rw-r--r-- root/root      2358 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd
-rw-r--r-- root/root       659 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_GBSeq.dtd
-rw-r--r-- root/root     11502 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd
-rw-r--r-- root/root       776 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Gene.dtd
-rw-r--r-- root/root      2381 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd
-rw-r--r-- root/root       671 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_General.dtd
-rw-r--r-- root/root      8215 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_General.mod.dtd
-rw-r--r-- root/root      3629 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID1Access.dtd
-rw-r--r-- root/root      5733 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd
-rw-r--r-- root/root      3757 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID2Access.dtd
-rw-r--r-- root/root     23205 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd
-rw-r--r-- root/root      1378 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_MedArchive.dtd
-rw-r--r-- root/root      6931 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd
-rw-r--r-- root/root       907 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medlars.dtd
-rw-r--r-- root/root      1617 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd
-rw-r--r-- root/root       907 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medline.dtd
-rw-r--r-- root/root      5757 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd
-rw-r--r-- root/root       647 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mim.dtd
-rw-r--r-- root/root      8395 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd
-rw-r--r-- root/root      4461 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mime.dtd
-rw-r--r-- root/root      7270 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd
-rw-r--r-- root/root       665 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd
-rw-r--r-- root/root      3131 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd
-rw-r--r-- root/root       796 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Organism.dtd
-rw-r--r-- root/root      5250 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd
-rw-r--r-- root/root      1519 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCAssay.dtd
-rw-r--r-- root/root     31800 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd
-rw-r--r-- root/root      1155 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd
-rw-r--r-- root/root     43623 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd
-rw-r--r-- root/root      3736 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Project.dtd
-rw-r--r-- root/root      3769 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Project.mod.dtd
-rw-r--r-- root/root       791 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Protein.dtd
-rw-r--r-- root/root      1791 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd
-rw-r--r-- root/root      1003 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Pub.dtd
-rw-r--r-- root/root      2700 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd
-rw-r--r-- root/root      1021 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PubMed.dtd
-rw-r--r-- root/root      1698 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd
-rw-r--r-- root/root      3383 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_RNA.dtd
-rw-r--r-- root/root      3379 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd
-rw-r--r-- root/root      3495 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Remap.dtd
-rw-r--r-- root/root      4064 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd
-rw-r--r-- root/root       781 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Rsite.dtd
-rw-r--r-- root/root      1044 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd
-rw-r--r-- root/root      3629 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd
-rw-r--r-- root/root     19503 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd
-rw-r--r-- root/root       671 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqCode.dtd
-rw-r--r-- root/root      4231 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd
-rw-r--r-- root/root      3389 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqTable.dtd
-rw-r--r-- root/root      9912 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd
-rw-r--r-- root/root      3634 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seq_split.dtd
-rw-r--r-- root/root     11475 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd
-rw-r--r-- root/root      3389 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqalign.dtd
-rw-r--r-- root/root     15026 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd
-rw-r--r-- root/root      3387 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd
-rw-r--r-- root/root     19204 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd
-rw-r--r-- root/root      3385 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqloc.dtd
-rw-r--r-- root/root      7383 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd
-rw-r--r-- root/root      3385 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqres.dtd
-rw-r--r-- root/root      3149 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd
-rw-r--r-- root/root      3501 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqset.dtd
-rw-r--r-- root/root      3479 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd
-rw-r--r-- root/root      3384 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Sequence.dtd
-rw-r--r-- root/root     26293 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd
-rw-r--r-- root/root      3617 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Submit.dtd
-rw-r--r-- root/root      4130 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd
-rw-r--r-- root/root      3379 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Systems.dtd
-rw-r--r-- root/root       656 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TSeq.dtd
-rw-r--r-- root/root      1660 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd
-rw-r--r-- root/root      1138 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TxInit.dtd
-rw-r--r-- root/root      4625 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd
-rw-r--r-- root/root      3389 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Variation.dtd
-rw-r--r-- root/root     27155 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd
-rw-r--r-- root/root      7893 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_all.dtd
-rw-r--r-- root/root       625 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NSE.dtd
-rw-r--r-- root/root     26853 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NSE.mod.dtd
-rw-r--r-- root/root      3470 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/OMSSA.dtd
-rw-r--r-- root/root     34917 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/OMSSA.mod.dtd
-rw-r--r-- root/root       787 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PDB_General.dtd
-rw-r--r-- root/root      1815 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PDB_General.mod.dtd
-rw-r--r-- root/root      3387 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PIR_General.dtd
-rw-r--r-- root/root      2076 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PIR_General.mod.dtd
-rw-r--r-- root/root       667 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PRF_General.dtd
-rw-r--r-- root/root      1535 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PRF_General.mod.dtd
-rw-r--r-- root/root      3386 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/SP_General.dtd
-rw-r--r-- root/root      2375 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/SP_General.mod.dtd
-rw-r--r-- root/root     17329 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/XHTMLtablesetup.ent
-rw-r--r-- root/root     51298 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivearticle.dtd
-rw-r--r-- root/root      8304 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-classes.ent
-rw-r--r-- root/root     16646 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-mixes.ent
-rw-r--r-- root/root     38921 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-models.ent
-rw-r--r-- root/root      6412 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-modules.ent
-rw-r--r-- root/root     98004 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/articlemeta.ent
-rw-r--r-- root/root     15090 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/backmatter.ent
-rw-r--r-- root/root      2645 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_100301.dtd
-rw-r--r-- root/root      2645 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_110101.dtd
-rw-r--r-- root/root      2645 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_120101.dtd
-rw-r--r-- root/root      2756 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_130101.dtd
-rw-r--r-- root/root      2756 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_140101.dtd
-rw-r--r-- root/root      2756 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_150101.dtd
-rw-r--r-- root/root     21412 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/chars.ent
-rw-r--r-- root/root    152388 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/common.ent
-rw-r--r-- root/root     33182 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/default-classes.ent
-rw-r--r-- root/root     19402 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/default-mixes.ent
-rw-r--r-- root/root     82067 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/display.ent
-rw-r--r-- root/root      1655 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eInfo_020511.dtd
-rw-r--r-- root/root      2299 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eLink_090910.dtd
-rw-r--r-- root/root      2447 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eLink_101123.dtd
-rw-r--r-- root/root       520 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/ePost_020511.dtd
-rw-r--r-- root/root      2392 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSearch_020511.dtd
-rw-r--r-- root/root       736 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSpell.dtd
-rw-r--r-- root/root       602 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSummary_041029.dtd
-rw-r--r-- root/root       851 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/egquery.dtd
-rw-r--r-- root/root      1715 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/einfo.dtd
-rw-r--r-- root/root      2447 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/elink.dtd
-rw-r--r-- root/root       466 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/elink_020122.dtd
-rw-r--r-- root/root       520 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/epost.dtd
-rw-r--r-- root/root      3337 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/esearch.dtd
-rw-r--r-- root/root       602 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/esummary-v1.dtd
-rw-r--r-- root/root      4163 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/esummary_gene.dtd
-rw-r--r-- root/root     22746 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/format.ent
-rw-r--r-- root/root      9849 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/htmltable.dtd
-rw-r--r-- root/root     11589 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsa.ent
-rw-r--r-- root/root      9556 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsb.ent
-rw-r--r-- root/root      2254 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsc.ent
-rw-r--r-- root/root      7945 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsn.ent
-rw-r--r-- root/root      4432 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamso.ent
-rw-r--r-- root/root     14133 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsr.ent
-rw-r--r-- root/root      3507 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isobox.ent
-rw-r--r-- root/root      5257 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isocyr1.ent
-rw-r--r-- root/root      2457 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isocyr2.ent
-rw-r--r-- root/root      1473 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isodia.ent
-rw-r--r-- root/root      4102 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk1.ent
-rw-r--r-- root/root      2389 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk2.ent
-rw-r--r-- root/root      3699 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk3.ent
-rw-r--r-- root/root      3591 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk4.ent
-rw-r--r-- root/root      5199 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isolat1.ent
-rw-r--r-- root/root      8865 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isolat2.ent
-rw-r--r-- root/root      4478 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomfrk.ent
-rw-r--r-- root/root      2522 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomopf.ent
-rw-r--r-- root/root      4557 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomscr.ent
-rw-r--r-- root/root      5816 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isonum.ent
-rw-r--r-- root/root      6594 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isopub.ent
-rw-r--r-- root/root     12399 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isotech.ent
-rw-r--r-- root/root     18988 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/journalmeta.ent
-rw-r--r-- root/root     28360 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/link.ent
-rw-r--r-- root/root     25663 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/list.ent
-rw-r--r-- root/root     18334 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/math.ent
-rw-r--r-- root/root      6820 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml-in-pubmed.mod
lrwxrwxrwx root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd -> ../../../../../../share/xml/w3c-sgml-lib/schema/dtd/XX-MathML2-20031104/mathml2.dtd
-rw-r--r-- root/root     12255 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml3-qname1.mod
-rw-r--r-- root/root     42407 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml3.dtd
-rw-r--r-- root/root     10452 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathmlsetup.ent
-rw-r--r-- root/root     37695 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mmlalias.ent
-rw-r--r-- root/root      7776 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mmlextra.ent
-rw-r--r-- root/root     21313 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/modules.ent
-rw-r--r-- root/root     35333 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd
-rw-r--r-- root/root     12369 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd
-rw-r--r-- root/root      5839 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_011101.dtd
-rw-r--r-- root/root      7946 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_080101.dtd
-rw-r--r-- root/root      8638 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_090101.dtd
-rw-r--r-- root/root      2053 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_011101.dtd
-rw-r--r-- root/root      3017 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_080101.dtd
-rw-r--r-- root/root      3195 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_090101.dtd
-rw-r--r-- root/root      6760 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd
-rw-r--r-- root/root      5001 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd
-rw-r--r-- root/root      5262 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd
-rw-r--r-- root/root      9322 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd
-rw-r--r-- root/root      9618 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd
-rw-r--r-- root/root      9308 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd
-rw-r--r-- root/root      8829 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd
-rw-r--r-- root/root      8995 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd
-rw-r--r-- root/root      9033 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd
-rw-r--r-- root/root      9112 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd
-rw-r--r-- root/root      8947 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd
-rw-r--r-- root/root      5672 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmserials_080101.dtd
-rw-r--r-- root/root      6703 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmserials_100101.dtd
-rw-r--r-- root/root      3185 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd
-rw-r--r-- root/root      3317 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd
-rw-r--r-- root/root      9656 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/notat.ent
-rw-r--r-- root/root     23807 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/para.ent
-rw-r--r-- root/root     15750 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/phrase.ent
-rw-r--r-- root/root     25142 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pmc-1.dtd
-rw-r--r-- root/root      2714 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_020114.dtd
-rw-r--r-- root/root      3045 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_080101.dtd
-rw-r--r-- root/root      3059 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_090101.dtd
-rw-r--r-- root/root      3126 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_100101.dtd
-rw-r--r-- root/root      3434 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_100301.dtd
-rw-r--r-- root/root      3434 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_110101.dtd
-rw-r--r-- root/root      3434 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_120101.dtd
-rw-r--r-- root/root      3434 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_130101.dtd
-rw-r--r-- root/root      3445 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_130501.dtd
-rw-r--r-- root/root      3445 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_140101.dtd
-rw-r--r-- root/root      3445 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_150101.dtd
-rw-r--r-- root/root     13062 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_180101.dtd
-rw-r--r-- root/root     13869 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_180601.dtd
-rw-r--r-- root/root     14576 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_190101.dtd
-rw-r--r-- root/root     40015 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/references.ent
-rw-r--r-- root/root     13173 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/section.ent
-rw-r--r-- root/root      4003 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/taxon.dtd
-rw-r--r-- root/root      1141 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod
-rw-r--r-- root/root      9503 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/xhtml-table-1.mod
-rw-r--r-- root/root     13595 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/xmlspecchars.ent
-rw-r--r-- root/root     44723 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/Parser.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Entrez/XSDs/
-rw-r--r-- root/root      3536 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/XSDs/IPGReportSet.xsd
-rw-r--r-- root/root     29953 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Entrez/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/ExPASy/
-rw-r--r-- root/root      4570 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/ExPASy/Enzyme.py
-rw-r--r-- root/root      5009 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/ExPASy/Prodoc.py
-rw-r--r-- root/root     11495 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/ExPASy/Prosite.py
-rw-r--r-- root/root      5146 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/ExPASy/ScanProsite.py
-rw-r--r-- root/root      4097 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/ExPASy/__init__.py
-rw-r--r-- root/root      6381 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/ExPASy/cellosaurus.py
-rw-r--r-- root/root     24673 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/File.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/GenBank/
-rw-r--r-- root/root     23278 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/GenBank/Record.py
-rw-r--r-- root/root     85906 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/GenBank/Scanner.py
-rw-r--r-- root/root     43868 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/GenBank/__init__.py
-rw-r--r-- root/root      2229 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/GenBank/utils.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Geo/
-rw-r--r-- root/root      2972 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Geo/Record.py
-rw-r--r-- root/root      2176 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Geo/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Graphics/
-rw-r--r-- root/root     31404 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/BasicChromosome.py
-rw-r--r-- root/root      7371 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/ColorSpiral.py
-rw-r--r-- root/root      6472 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py
-rw-r--r-- root/root      6775 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/DisplayRepresentation.py
-rw-r--r-- root/root      9334 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/
-rw-r--r-- root/root     18530 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py
-rw-r--r-- root/root     68538 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py
-rw-r--r-- root/root      9678 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Colors.py
-rw-r--r-- root/root      3309 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py
-rw-r--r-- root/root     15633 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Diagram.py
-rw-r--r-- root/root      8047 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Feature.py
-rw-r--r-- root/root      7802 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py
-rw-r--r-- root/root      6861 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Graph.py
-rw-r--r-- root/root      5634 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py
-rw-r--r-- root/root     63150 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py
-rw-r--r-- root/root     11663 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Track.py
-rw-r--r-- root/root      1172 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/__init__.py
-rw-r--r-- root/root     17644 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/KGML_vis.py
-rw-r--r-- root/root      3232 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Graphics/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/HMM/
-rw-r--r-- root/root     12483 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/HMM/DynamicProgramming.py
-rw-r--r-- root/root     26511 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/HMM/MarkovModel.py
-rw-r--r-- root/root     16472 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/HMM/Trainer.py
-rw-r--r-- root/root      2106 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/HMM/Utilities.py
-rw-r--r-- root/root       283 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/HMM/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/KEGG/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/KEGG/Compound/
-rw-r--r-- root/root      5412 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/Compound/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/KEGG/Enzyme/
-rw-r--r-- root/root     11127 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/Enzyme/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/KEGG/Gene/
-rw-r--r-- root/root      4250 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/Gene/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/
-rw-r--r-- root/root      6195 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/KGML_parser.py
-rw-r--r-- root/root     27604 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/KGML_pathway.py
-rw-r--r-- root/root       516 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/KEGG/Map/
-rw-r--r-- root/root      1642 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/Map/__init__.py
-rw-r--r-- root/root     10967 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/REST.py
-rw-r--r-- root/root      3039 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/KEGG/__init__.py
-rw-r--r-- root/root      4259 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/LogisticRegression.py
-rw-r--r-- root/root     23626 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/MarkovModel.py
-rw-r--r-- root/root     10881 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/MaxEntropy.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Medline/
-rw-r--r-- root/root      6000 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Medline/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/NMR/
-rw-r--r-- root/root      3353 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/NMR/NOEtools.py
-rw-r--r-- root/root       332 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/NMR/__init__.py
-rw-r--r-- root/root      9276 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/NMR/xpktools.py
-rw-r--r-- root/root      7962 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/NaiveBayes.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Nexus/
-rw-r--r-- root/root     84776 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py
-rw-r--r-- root/root      5745 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Nexus/Nodes.py
-rw-r--r-- root/root      4006 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Nexus/StandardData.py
-rw-r--r-- root/root     39870 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Nexus/Trees.py
-rw-r--r-- root/root       388 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Nexus/__init__.py
-rw-r--r-- root/root      3737 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Nexus/cnexus.c
-rw-r--r-- root/root      5604 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/PDB/
-rw-r--r-- root/root      4083 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/AbstractPropertyMap.py
-rw-r--r-- root/root     18337 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Atom.py
-rw-r--r-- root/root      6767 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Chain.py
-rw-r--r-- root/root     20286 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/DSSP.py
-rw-r--r-- root/root      2315 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Dice.py
-rw-r--r-- root/root     15259 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Entity.py
-rw-r--r-- root/root      9640 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/FragmentMapper.py
-rw-r--r-- root/root     11321 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/HSExposure.py
-rw-r--r-- root/root      4883 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/MMCIF2Dict.py
-rw-r--r-- root/root     24301 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/MMCIFParser.py
-rw-r--r-- root/root      2203 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Model.py
-rw-r--r-- root/root      7182 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/NACCESS.py
-rw-r--r-- root/root      4437 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/NeighborSearch.py
-rw-r--r-- root/root       897 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/PDBExceptions.py
-rw-r--r-- root/root     13553 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/PDBIO.py
-rw-r--r-- root/root     30861 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/PDBList.py
-rw-r--r-- root/root     17451 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py
-rw-r--r-- root/root     40896 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/PICIO.py
-rw-r--r-- root/root      3100 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/PSEA.py
-rw-r--r-- root/root     15215 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Polypeptide.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/
-rw-r--r-- root/root      5590 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/__init__.py
-rw-r--r-- root/root      9125 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.c
-rw-r--r-- root/root      9700 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so
-rw-r--r-- root/root      5262 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Residue.py
-rw-r--r-- root/root     22268 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/ResidueDepth.py
-rw-r--r-- root/root      8435 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/SASA.py
-rw-r--r-- root/root     34578 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/SCADIO.py
-rw-r--r-- root/root      2591 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Selection.py
-rw-r--r-- root/root      2043 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Structure.py
-rw-r--r-- root/root      3340 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/StructureAlignment.py
-rw-r--r-- root/root     11708 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py
-rw-r--r-- root/root      1947 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/Superimposer.py
-rw-r--r-- root/root      2499 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/__init__.py
-rw-r--r-- root/root      9700 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so
-rw-r--r-- root/root     23585 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/ccealignmodule.c
-rw-r--r-- root/root      5513 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/cealign.py
-rw-r--r-- root/root     59188 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/ic_data.py
-rw-r--r-- root/root     18541 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/ic_rebuild.py
-rw-r--r-- root/root    187233 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/internal_coords.py
-rw-r--r-- root/root     42796 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/kdtrees.c
-rw-r--r-- root/root     18912 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so
-rw-r--r-- root/root     15410 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/mmcifio.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/
-rw-r--r-- root/root      8949 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/DefaultParser.py
-rw-r--r-- root/root      1546 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/__init__.py
-rw-r--r-- root/root     10193 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/mmtfio.py
-rw-r--r-- root/root     11694 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/parse_pdb_header.py
-rw-r--r-- root/root     11906 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/qcprot.py
-rw-r--r-- root/root     20603 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PDB/vectors.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Pathway/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/
-rw-r--r-- root/root      5865 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/Graph.py
-rw-r--r-- root/root      6779 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/MultiGraph.py
-rw-r--r-- root/root       575 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/__init__.py
-rw-r--r-- root/root     10763 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Pathway/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Phylo/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/
-rw-r--r-- root/root     27405 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Fasttree.py
-rw-r--r-- root/root     10846 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Phyml.py
-rw-r--r-- root/root     18861 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Raxml.py
-rw-r--r-- root/root       751 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/__init__.py
-rw-r--r-- root/root     44970 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/BaseTree.py
-rw-r--r-- root/root      1662 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/CDAO.py
-rw-r--r-- root/root     16045 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py
-rw-r--r-- root/root     24309 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/Consensus.py
-rw-r--r-- root/root      1404 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/NeXML.py
-rw-r--r-- root/root     11326 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/NeXMLIO.py
-rw-r--r-- root/root      1298 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/Newick.py
-rw-r--r-- root/root     12517 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/NewickIO.py
-rw-r--r-- root/root      2652 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/NexusIO.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/
-rw-r--r-- root/root       325 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/__init__.py
-rw-r--r-- root/root      5145 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_paml.py
-rw-r--r-- root/root     11409 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_baseml.py
-rw-r--r-- root/root     21155 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_codeml.py
-rw-r--r-- root/root      6820 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_yn00.py
-rw-r--r-- root/root      8272 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/baseml.py
-rw-r--r-- root/root      3727 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/chi2.py
-rw-r--r-- root/root      8844 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/codeml.py
-rw-r--r-- root/root      5731 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/yn00.py
-rw-r--r-- root/root     46738 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py
-rw-r--r-- root/root     32752 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py
-rw-r--r-- root/root     49226 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/TreeConstruction.py
-rw-r--r-- root/root       513 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/__init__.py
-rw-r--r-- root/root    109268 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/_cdao_owl.py
-rw-r--r-- root/root      2595 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/_io.py
-rw-r--r-- root/root     17879 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Phylo/_utils.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/PopGen/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/
-rw-r--r-- root/root     34382 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/Controller.py
-rw-r--r-- root/root      7789 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/EasyController.py
-rw-r--r-- root/root     11860 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/FileParser.py
-rw-r--r-- root/root      3919 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/LargeFileParser.py
-rw-r--r-- root/root      7461 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/__init__.py
-rw-r--r-- root/root       359 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/PopGen/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Restriction/
-rw-r--r-- root/root     16299 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Restriction/PrintFormat.py
-rw-r--r-- root/root     85184 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Restriction/Restriction.py
-rw-r--r-- root/root    550284 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Restriction/Restriction_Dictionary.py
-rw-r--r-- root/root      7837 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Restriction/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SCOP/
-rw-r--r-- root/root      3922 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SCOP/Cla.py
-rw-r--r-- root/root      3004 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SCOP/Des.py
-rw-r--r-- root/root      2466 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SCOP/Dom.py
-rw-r--r-- root/root      2963 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SCOP/Hie.py
-rw-r--r-- root/root     10338 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SCOP/Raf.py
-rw-r--r-- root/root      3084 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SCOP/Residues.py
-rw-r--r-- root/root     32757 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SCOP/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SVDSuperimposer/
-rw-r--r-- root/root      6211 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SVDSuperimposer/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SearchIO/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/
-rw-r--r-- root/root     23895 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/__init__.py
-rw-r--r-- root/root     33733 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_tab.py
-rw-r--r-- root/root      5610 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_text.py
-rw-r--r-- root/root     36938 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_xml.py
-rw-r--r-- root/root     31231 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlatIO.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/
-rw-r--r-- root/root     12964 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/__init__.py
-rw-r--r-- root/root     20876 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/_base.py
-rw-r--r-- root/root      4089 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py
-rw-r--r-- root/root     20434 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py
-rw-r--r-- root/root      8244 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py
-rw-r--r-- root/root     25906 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/FastaIO.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/
-rw-r--r-- root/root       639 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/__init__.py
-rw-r--r-- root/root      9261 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/
-rw-r--r-- root/root     20309 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/__init__.py
-rw-r--r-- root/root      1482 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/_base.py
-rw-r--r-- root/root     12839 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py
-rw-r--r-- root/root     13956 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py
-rw-r--r-- root/root     12818 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py
-rw-r--r-- root/root     18733 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/
-rw-r--r-- root/root      5155 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/__init__.py
-rw-r--r-- root/root      7455 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py
-rw-r--r-- root/root     28939 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/__init__.py
-rw-r--r-- root/root      1213 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_index.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/
-rw-r--r-- root/root     74634 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/NCBIStandalone.py
-rw-r--r-- root/root     12123 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/ParserSupport.py
-rw-r--r-- root/root       690 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/
-rw-r--r-- root/root      2464 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/__init__.py
-rw-r--r-- root/root      2626 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/_base.py
-rw-r--r-- root/root     17335 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/hit.py
-rw-r--r-- root/root     48190 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/hsp.py
-rw-r--r-- root/root     30200 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/query.py
-rw-r--r-- root/root      5584 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SearchIO/_utils.py
-rw-r--r-- root/root    118856 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Seq.py
-rw-r--r-- root/root     94308 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqFeature.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SeqIO/
-rw-r--r-- root/root     26087 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/AbiIO.py
-rw-r--r-- root/root      4091 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/AceIO.py
-rw-r--r-- root/root     16504 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/FastaIO.py
-rw-r--r-- root/root      8069 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/GckIO.py
-rw-r--r-- root/root      4433 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/IgIO.py
-rw-r--r-- root/root     56731 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py
-rw-r--r-- root/root      9168 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/Interfaces.py
-rw-r--r-- root/root      5841 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/NibIO.py
-rw-r--r-- root/root     20579 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/PdbIO.py
-rw-r--r-- root/root      6059 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/PhdIO.py
-rw-r--r-- root/root     10295 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/PirIO.py
-rw-r--r-- root/root     91857 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/QualityIO.py
-rw-r--r-- root/root     27263 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/SeqXmlIO.py
-rw-r--r-- root/root     55630 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/SffIO.py
-rw-r--r-- root/root     10978 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/SnapGeneIO.py
-rw-r--r-- root/root      4817 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/SwissIO.py
-rw-r--r-- root/root      5014 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/TabIO.py
-rw-r--r-- root/root     11060 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py
-rw-r--r-- root/root     25411 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/UniprotIO.py
-rw-r--r-- root/root     12533 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/XdnaIO.py
-rw-r--r-- root/root     43507 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py
-rw-r--r-- root/root     27358 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/_index.py
-rw-r--r-- root/root     21992 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.c
-rw-r--r-- root/root      9896 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so
-rw-r--r-- root/root     55567 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqRecord.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SeqUtils/
-rw-r--r-- root/root      3511 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CheckSum.py
-rw-r--r-- root/root      7199 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CodonUsage.py
-rw-r--r-- root/root      1983 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CodonUsageIndices.py
-rw-r--r-- root/root      6557 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/IsoelectricPoint.py
-rw-r--r-- root/root     43142 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/MeltingTemp.py
-rw-r--r-- root/root     13021 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/ProtParam.py
-rw-r--r-- root/root     18172 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/ProtParamData.py
-rw-r--r-- root/root     23125 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/__init__.py
-rw-r--r-- root/root      5502 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SeqUtils/lcc.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Sequencing/
-rw-r--r-- root/root     20709 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Sequencing/Ace.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/
-rw-r--r-- root/root      8586 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_Novoalign.py
-rw-r--r-- root/root      2189 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/__init__.py
-rw-r--r-- root/root     28256 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_bwa.py
-rw-r--r-- root/root     36658 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_samtools.py
-rw-r--r-- root/root      5685 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Sequencing/Phd.py
-rw-r--r-- root/root       530 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Sequencing/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/SwissProt/
-rw-r--r-- root/root      3468 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SwissProt/KeyWList.py
-rw-r--r-- root/root     32856 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/SwissProt/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/TogoWS/
-rw-r--r-- root/root     13889 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/TogoWS/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/UniGene/
-rw-r--r-- root/root     12738 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/UniGene/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/UniProt/
-rw-r--r-- root/root     15792 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/UniProt/GOA.py
-rw-r--r-- root/root       722 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/UniProt/__init__.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/Wise/
-rw-r--r-- root/root      4909 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Wise/__init__.py
-rw-r--r-- root/root      4802 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Wise/dnal.py
-rw-r--r-- root/root      4604 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/Wise/psw.py
-rw-r--r-- root/root      5399 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/__init__.py
-rw-r--r-- root/root      2095 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/_utils.py
-rw-r--r-- root/root     39444 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/bgzf.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/codonalign/
-rw-r--r-- root/root     30013 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/codonalign/__init__.py
-rw-r--r-- root/root     18030 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/codonalign/codonalignment.py
-rw-r--r-- root/root     47867 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/codonalign/codonseq.py
-rw-r--r-- root/root      9824 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so
-rw-r--r-- root/root     16043 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/cpairwise2module.c
-rw-r--r-- root/root      4296 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/kNN.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/motifs/
-rw-r--r-- root/root     21230 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/__init__.py
-rw-r--r-- root/root      5800 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/_pwm.c
-rw-r--r-- root/root      9936 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so
-rw-r--r-- root/root      2107 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/alignace.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/motifs/applications/
-rw-r--r-- root/root       582 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/applications/__init__.py
-rw-r--r-- root/root     10382 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/applications/_xxmotif.py
-rw-r--r-- root/root      2609 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/clusterbuster.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/
-rw-r--r-- root/root     11305 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/__init__.py
-rw-r--r-- root/root     27885 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/db.py
-rw-r--r-- root/root      4915 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/mast.py
-rw-r--r-- root/root     20572 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/matrix.py
-rw-r--r-- root/root      6803 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/meme.py
-rw-r--r-- root/root      5855 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/minimal.py
-rw-r--r-- root/root     16521 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/pfm.py
-rw-r--r-- root/root      4530 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/thresholds.py
-rw-r--r-- root/root     11897 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/transfac.py
-rw-r--r-- root/root      3924 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/motifs/xms.py
-rw-r--r-- root/root     53156 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/pairwise2.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/Bio/phenotype/
-rw-r--r-- root/root      8020 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/phenotype/__init__.py
-rw-r--r-- root/root     37605 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/phenotype/phen_micro.py
-rw-r--r-- root/root      4062 2023-02-13 03:07 ./usr/lib/python3/dist-packages/Bio/phenotype/pm_fitting.py
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/biopython-1.81.egg-info/
-rw-r--r-- root/root     13112 2023-11-11 10:16 ./usr/lib/python3/dist-packages/biopython-1.81.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2023-11-11 10:16 ./usr/lib/python3/dist-packages/biopython-1.81.egg-info/dependency_links.txt
-rw-r--r-- root/root         0 2023-11-11 10:16 ./usr/lib/python3/dist-packages/biopython-1.81.egg-info/requires.txt
-rw-r--r-- root/root        11 2023-11-11 10:16 ./usr/lib/python3/dist-packages/biopython-1.81.egg-info/top_level.txt
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/share/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/share/doc/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/share/doc/python3-biopython/
-rw-r--r-- root/root      5559 2023-02-13 03:07 ./usr/share/doc/python3-biopython/CONTRIB.rst.gz
-rw-r--r-- root/root      3957 2023-02-13 03:07 ./usr/share/doc/python3-biopython/CONTRIBUTING.rst
-rw-r--r-- root/root      8942 2023-02-13 03:07 ./usr/share/doc/python3-biopython/DEPRECATED.rst.gz
-rw-r--r-- root/root       429 2023-11-11 10:16 ./usr/share/doc/python3-biopython/NEWS.Debian.gz
-rw-r--r-- root/root     38485 2023-02-13 03:07 ./usr/share/doc/python3-biopython/NEWS.rst.gz
-rw-r--r-- root/root       273 2023-11-11 10:16 ./usr/share/doc/python3-biopython/README.Debian
-rw-r--r-- root/root      4289 2023-11-11 10:16 ./usr/share/doc/python3-biopython/changelog.Debian.gz
-rw-r--r-- root/root      2117 2023-11-11 10:16 ./usr/share/doc/python3-biopython/copyright
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/share/lintian/
drwxr-xr-x root/root         0 2023-11-11 10:16 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       188 2023-11-11 10:16 ./usr/share/lintian/overrides/python3-biopython


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build Type: any
Build-Space: 371344
Build-Time: 639
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 433
Job: python-biopython_1.81+dfsg-2
Machine Architecture: arm64
Package: python-biopython
Package-Time: 1083
Source-Version: 1.81+dfsg-2
Space: 371344
Status: successful
Version: 1.81+dfsg-2
--------------------------------------------------------------------------------
Finished at 2023-11-14T07:12:19Z
Build needed 00:18:03, 371344k disk space