Raspbian Package Auto-Building

Build log for python-biopython (1.79+dfsg-1) on armhf

python-biopython1.79+dfsg-1armhf → 2021-10-25 07:35:34

sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019

+==============================================================================+
| python-biopython 1.79+dfsg-1 (armhf)         Mon, 25 Oct 2021 06:40:41 +0000 |
+==============================================================================+

Package: python-biopython
Version: 1.79+dfsg-1
Source Version: 1.79+dfsg-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-29ba56e0-c33c-4894-a9a2-7530756e1b17' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/python-biopython-X66SbR/resolver-soJHLE' with '<<RESOLVERDIR>>'

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

Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 11s (2333 kB/s)
Reading package lists...

+------------------------------------------------------------------------------+
| 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 9883 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main python-biopython 1.79+dfsg-1 (dsc) [3224 B]
Get:2 http://172.17.0.1/private bookworm-staging/main python-biopython 1.79+dfsg-1 (tar) [9861 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main python-biopython 1.79+dfsg-1 (diff) [18.3 kB]
Fetched 9883 kB in 1s (7355 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-biopython-X66SbR/python-biopython-1.79+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-biopython-X66SbR' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-renderpm, python3-psycopg2, python3-pygments, python3-scipy, python3-setuptools, python3-unittest2, samtools, t-coffee, wise, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy, flex, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, bwa, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle, ncbi-blast+, phylip, prank, probcons, python3-networkx, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-renderpm, 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 [963 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [643 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [678 B]
Fetched 2284 B in 0s (59.5 kB/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 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-lmodern fonts-lyx fonts-urw-base35 gcc-11-base gettext gettext-base
  ghostscript groff-base hevea intltool-debian libapache-pom-java
  libarchive-zip-perl libargtable2-0 libasan6 libatomic1 libavahi-client3
  libavahi-common-data libavahi-common3 libblas3 libboost-iostreams1.74.0
  libboost-program-options1.74.0 libbrotli1 libbsd0 libcairo2 libcc1-0
  libcifpp1 libcommons-logging-java libcommons-parent-java libcups2
  libcurl3-gnutls libdbus-1-3 libdebhelper-perl libdeflate0 libelf1 libexpat1
  libexpat1-dev libffi8 libfile-stripnondeterminism-perl libfontbox-java
  libfontconfig1 libfreetype6 libfribidi0 libgcc-s1 libgd3 libgfortran5
  libglib2.0-0 libgomp1 libgraphite2-3 libgs9 libgs9-common libharfbuzz0b
  libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu67 libidn12 libijs-0.35
  libimagequant0 libjbig0 libjbig2dec0 libjpeg62-turbo libjs-jquery
  libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3
  liblbfgsb0 liblcms2-2 liblmdb0 libmagic-mgc libmagic1 libmariadb3
  libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmpdec3 libncurses6
  libnetpbm10 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1
  libpdfbox-java libpipeline1 libpixman-1-0 libpng16-16 libpq5 libpsl5
  libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.9
  libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libraqm0 librtmp1
  libsigsegv2 libsm6 libssh2-1 libstdc++6 libsub-override-perl libsynctex2
  libteckit0 libtexlua53 libtexluajit2 libtiff5 libtool libubsan1 libuchardet0
  libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6
  libxpm4 libxrender1 libxt6 libzzip-0-13 m4 mafft mailcap man-db
  mariadb-common media-types mime-support muscle 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-cycler python3-dateutil python3-decorator python3-dev
  python3-distutils python3-isodate python3-kiwisolver python3-lib2to3
  python3-linecache2 python3-matplotlib python3-minimal python3-mmtf
  python3-msgpack python3-mysqldb python3-networkx python3-numpy python3-pil
  python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing
  python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel
  python3-scipy python3-setuptools python3-six python3-traceback2
  python3-unittest2 python3.9 python3.9-dev python3.9-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 ttf-bitstream-vera ucf wise
  wise-data x11-common xdg-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc clustalx seaview dh-make flit
  python3-toml emboss-doc emboss-test embassy bison flex-doc
  fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc
  libasprintf-dev libgettextpo-dev ghostscript-x groff hevea-doc
  libavalon-framework-java libcommons-logging-java-doc
  libexcalibur-logkit-java liblog4j1.2-java cups-common libgd-tools
  libjs-jquery-ui-docs liblcms2-utils 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-tk
  python3-venv python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 inkscape
  ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi
  python3-gi-cairo python3-gobject python3-nose python3-pyqt5 python3-sip
  python3-tornado texlive-extra-utils ttf-staypuft default-mysql-server
  | virtual-mysql-server python3-mysqldb-dbg python-networkx-doc gfortran
  python-numpy-doc python3-numpy-dbg python3-pytest python-pil-doc
  python-psycopg2-doc python-pygments-doc python-pyparsing-doc
  python-rdflib-doc python3-renderpm-dbg pdf-viewer python3-egenix-mxtexttools
  python-reportlab-doc python-scipy-doc python-setuptools-doc python3.9-venv
  python3.9-doc binfmt-support cwltool boxshade t-coffee-examples perl-tk xpdf
  | pdf-viewer xzdec texlive-fonts-recommended-doc texlive-latex-base-doc
  icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl
  texlive-latex-extra-doc texlive-latex-recommended-doc texlive-luatex
  texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby
  texlive-pictures-doc vprerex wise-doc
Recommended packages:
  primer3 libfl-dev curl | wget | lynx ca-certificates dbus
  libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs
  fonts-droid-fallback javascript-common libgpm2 publicsuffix libltdl-dev
  blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-tk python3-gdal
  python3-pydot python3-pygraphviz python3-yaml python3-olefile
  python3-sparqlwrapper python3-html5lib amap-align dialign-tx fsa kalign
  libsoap-lite-perl libxml-simple-perl mustang poa proda tm-align lmodern
  dvisvgm tex-gyre tipa 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 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-lmodern fonts-lyx fonts-urw-base35 gettext gettext-base ghostscript
  groff-base hevea intltool-debian libapache-pom-java libarchive-zip-perl
  libargtable2-0 libavahi-client3 libavahi-common-data libavahi-common3
  libblas3 libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1
  libbsd0 libcairo2 libcifpp1 libcommons-logging-java libcommons-parent-java
  libcups2 libcurl3-gnutls libdbus-1-3 libdebhelper-perl libdeflate0 libelf1
  libexpat1 libexpat1-dev libffi8 libfile-stripnondeterminism-perl
  libfontbox-java libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5
  libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libharfbuzz0b libhpdf-2.3.0
  libhts3 libhtscodecs2 libice6 libicu67 libidn12 libijs-0.35 libimagequant0
  libjbig0 libjbig2dec0 libjpeg62-turbo libjs-jquery libjs-jquery-ui
  libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0
  liblcms2-2 liblmdb0 libmagic-mgc libmagic1 libmariadb3 libmbedcrypto3
  libmbedtls12 libmbedx509-0 libmd0 libmpdec3 libncurses6 libnetpbm10
  libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java
  libpipeline1 libpixman-1-0 libpng16-16 libpq5 libpsl5 libptexenc1
  libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.9
  libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libraqm0 librtmp1
  libsigsegv2 libsm6 libssh2-1 libsub-override-perl libsynctex2 libteckit0
  libtexlua53 libtexluajit2 libtiff5 libtool libuchardet0 libwebp6
  libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6
  libxpm4 libxrender1 libxt6 libzzip-0-13 m4 mafft mailcap man-db
  mariadb-common media-types mime-support muscle 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-cycler python3-dateutil python3-decorator python3-dev
  python3-distutils python3-isodate python3-kiwisolver python3-lib2to3
  python3-linecache2 python3-matplotlib python3-minimal python3-mmtf
  python3-msgpack python3-mysqldb python3-networkx python3-numpy python3-pil
  python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing
  python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel
  python3-scipy python3-setuptools python3-six python3-traceback2
  python3-unittest2 python3.9 python3.9-dev python3.9-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
  ttf-bitstream-vera ucf wise wise-data x11-common xdg-utils zlib1g-dev
The following packages will be upgraded:
  gcc-11-base libasan6 libatomic1 libcc1-0 libgcc-s1 libgomp1 libstdc++6
  libubsan1
8 upgraded, 222 newly installed, 0 to remove and 33 not upgraded.
Need to get 257 MB of archives.
After this operation, 1212 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1104 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-3 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-9+rpi1 [1947 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-9+rpi1 [798 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-9+rpi1 [88.0 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-9+rpi1 [206 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-9+rpi1 [36.2 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-9+rpi1 [38.0 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-9+rpi1 [8184 B]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-9+rpi1 [466 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf flex armhf 2.6.4-8 [412 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf poppler-data all 0.4.11-1 [1608 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf mailcap all 3.70 [31.8 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-3 [21.3 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf tex-common all 6.17 [53.6 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1 [823 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf bwa armhf 0.7.17-6 [195 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libargtable2-0 armhf 13-1.1 [15.9 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf clustalo armhf 1.2.4-7 [222 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf clustalw armhf 2.1+lgpl-7 [229 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.7-1 [79.4 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf python3-distutils all 3.9.7-1 [146 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf dh-python all 5.20211016.1 [103 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf dialign armhf 2.2.1-11 [134 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-9 [260 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libboost-program-options1.74.0 armhf 1.74.0-9 [334 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libcifpp1 armhf 1.0.1-3 [1316 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf dssp armhf 4.0.0-2 [101 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libfreetype6 armhf 2.11.0+dfsg-1 [386 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf ttf-bitstream-vera all 1.10-8.1 [223 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf fonts-urw-base35 all 20200910-1 [6367 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [122 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libwebp6 armhf 0.6.1-2.1 [225 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libtiff5 armhf 4.3.0-2 [272 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf libxpm4 armhf 1:3.5.12-1 [43.6 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libgd3 armhf 2.3.0-2 [116 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libhpdf-2.3.0 armhf 2.3.0+dfsg-1 [330 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf mysql-common all 5.8+1.0.7 [7464 B]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf mariadb-common all 1:10.5.12-1 [36.3 kB]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libmariadb3 armhf 1:10.5.12-1 [160 kB]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf libpq5 armhf 14.0-1 [151 kB]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf emboss-lib armhf 6.6.0+dfsg-9 [2601 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf emboss-data all 6.6.0+dfsg-9 [61.1 MB]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf emboss armhf 6.6.0+dfsg-9 [1008 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf fasttree armhf 2.1.11-2 [158 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf fonts-lmodern all 2.004.5-6.1 [4540 kB]
Get:101 http://172.17.0.1/private bookworm-staging/main armhf fonts-lyx all 2.3.6-1 [205 kB]
Get:102 http://172.17.0.1/private bookworm-staging/main armhf libgs9-common all 9.54.0~dfsg-5 [740 kB]
Get:103 http://172.17.0.1/private bookworm-staging/main armhf libavahi-common-data armhf 0.8-5 [123 kB]
Get:104 http://172.17.0.1/private bookworm-staging/main armhf libavahi-common3 armhf 0.8-5 [55.3 kB]
Get:105 http://172.17.0.1/private bookworm-staging/main armhf libdbus-1-3 armhf 1.12.20-2 [193 kB]
Get:106 http://172.17.0.1/private bookworm-staging/main armhf libavahi-client3 armhf 0.8-5 [57.9 kB]
Get:107 http://172.17.0.1/private bookworm-staging/main armhf libcups2 armhf 2.3.3op2-7 [312 kB]
Get:108 http://172.17.0.1/private bookworm-staging/main armhf libidn12 armhf 1.38-3 [80.9 kB]
Get:109 http://172.17.0.1/private bookworm-staging/main armhf libijs-0.35 armhf 0.35-15 [14.7 kB]
Get:110 http://172.17.0.1/private bookworm-staging/main armhf libjbig2dec0 armhf 0.19-3 [58.3 kB]
Get:111 http://172.17.0.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.12~rc1-2 [121 kB]
Get:112 http://172.17.0.1/private bookworm-staging/main armhf libopenjp2-7 armhf 2.4.0-3 [150 kB]
Get:113 http://172.17.0.1/private bookworm-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:114 http://172.17.0.1/private bookworm-staging/main armhf libgs9 armhf 9.54.0~dfsg-5 [1900 kB]
Get:115 http://172.17.0.1/private bookworm-staging/main armhf ghostscript armhf 9.54.0~dfsg-5 [98.2 kB]
Get:116 http://172.17.0.1/private bookworm-staging/main armhf libnetpbm10 armhf 2:10.0-15.4 [75.4 kB]
Get:117 http://172.17.0.1/private bookworm-staging/main armhf netpbm armhf 2:10.0-15.4 [875 kB]
Get:118 http://172.17.0.1/private bookworm-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:119 http://172.17.0.1/private bookworm-staging/main armhf libkpathsea6 armhf 2021.20210626.59705-1 [164 kB]
Get:120 http://172.17.0.1/private bookworm-staging/main armhf libptexenc1 armhf 2021.20210626.59705-1 [61.5 kB]
Get:121 http://172.17.0.1/private bookworm-staging/main armhf libsynctex2 armhf 2021.20210626.59705-1 [67.4 kB]
Get:122 http://172.17.0.1/private bookworm-staging/main armhf libtexlua53 armhf 2021.20210626.59705-1 [102 kB]
Get:123 http://172.17.0.1/private bookworm-staging/main armhf libtexluajit2 armhf 2021.20210626.59705-1 [208 kB]
Get:124 http://172.17.0.1/private bookworm-staging/main armhf t1utils armhf 1.41-4 [52.3 kB]
Get:125 http://172.17.0.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:126 http://172.17.0.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.14-3 [110 kB]
Get:127 http://172.17.0.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.14-3 [101 kB]
Get:128 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:129 http://172.17.0.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:130 http://172.17.0.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-5 [602 kB]
Get:131 http://172.17.0.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:132 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:133 http://172.17.0.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:134 http://172.17.0.1/private bookworm-staging/main armhf libteckit0 armhf 2.5.10+ds1-3 [252 kB]
Get:135 http://172.17.0.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:136 http://172.17.0.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:137 http://172.17.0.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:138 http://172.17.0.1/private bookworm-staging/main armhf libxt6 armhf 1:1.2.0-1 [159 kB]
Get:139 http://172.17.0.1/private bookworm-staging/main armhf libxmu6 armhf 2:1.1.2-2+b3 [52.1 kB]
Get:140 http://172.17.0.1/private bookworm-staging/main armhf libxaw7 armhf 2:1.0.13-1.1 [166 kB]
Get:141 http://172.17.0.1/private bookworm-staging/main armhf libxi6 armhf 2:1.8-1 [78.1 kB]
Get:142 http://172.17.0.1/private bookworm-staging/main armhf libzzip-0-13 armhf 0.13.72+dfsg.1-1.1 [54.3 kB]
Get:143 http://172.17.0.1/private bookworm-staging/main armhf texlive-binaries armhf 2021.20210626.59705-1 [6847 kB]
Get:144 http://172.17.0.1/private bookworm-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:145 http://172.17.0.1/private bookworm-staging/main armhf texlive-base all 2021.20210921-1 [21.1 MB]
Get:146 http://172.17.0.1/private bookworm-staging/main armhf hevea armhf 2.35-1 [1677 kB]
Get:147 http://172.17.0.1/private bookworm-staging/main armhf libapache-pom-java all 18-1 [4676 B]
Get:148 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-1 [108 kB]
Get:149 http://172.17.0.1/private bookworm-staging/main armhf libcommons-parent-java all 43-1 [10.8 kB]
Get:150 http://172.17.0.1/private bookworm-staging/main armhf libcommons-logging-java all 1.2-2 [62.2 kB]
Get:151 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:152 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:153 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:154 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:155 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:156 http://172.17.0.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.1-2 [135 kB]
Get:157 http://172.17.0.1/private bookworm-staging/main armhf libfontbox-java all 1:1.8.16-2 [211 kB]
Get:158 http://172.17.0.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:159 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-9+rpi1 [235 kB]
Get:160 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:161 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:162 http://172.17.0.1/private bookworm-staging/main armhf libimagequant0 armhf 2.12.2-1.1 [27.2 kB]
Get:163 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:164 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get:165 http://172.17.0.1/private bookworm-staging/main armhf libjs-underscore all 1.9.1~dfsg-4 [100 kB]
Get:166 http://172.17.0.1/private bookworm-staging/main armhf libjs-sphinxdoc all 4.2.0-4 [137 kB]
Get:167 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.0-1 [1594 kB]
Get:168 http://172.17.0.1/private bookworm-staging/main armhf liblbfgsb0 armhf 3.0+dfsg.3-9 [24.6 kB]
Get:169 http://172.17.0.1/private bookworm-staging/main armhf liblmdb0 armhf 0.9.24-1 [38.7 kB]
Get:170 http://172.17.0.1/private bookworm-staging/main armhf libmbedcrypto3 armhf 2.16.9-0.1 [196 kB]
Get:171 http://172.17.0.1/private bookworm-staging/main armhf libmbedx509-0 armhf 2.16.9-0.1 [104 kB]
Get:172 http://172.17.0.1/private bookworm-staging/main armhf libmbedtls12 armhf 2.16.9-0.1 [132 kB]
Get:173 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:174 http://172.17.0.1/private bookworm-staging/main armhf libpdfbox-java all 1:1.8.16-2 [5205 kB]
Get:175 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9 armhf 3.9.7-4+rpi1 [1416 kB]
Get:176 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:177 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-dev armhf 3.9.7-4+rpi1 [3060 kB]
Get:178 http://172.17.0.1/private bookworm-staging/main armhf libpython3-dev armhf 3.9.2-3 [21.7 kB]
Get:179 http://172.17.0.1/private bookworm-staging/main armhf libpython3-all-dev armhf 3.9.2-3 [1068 B]
Get:180 http://172.17.0.1/private bookworm-staging/main armhf libraqm0 armhf 0.7.0-4 [9388 B]
Get:181 http://172.17.0.1/private bookworm-staging/main armhf libwebpdemux2 armhf 0.6.1-2.1 [86.8 kB]
Get:182 http://172.17.0.1/private bookworm-staging/main armhf libwebpmux3 armhf 0.6.1-2.1 [94.4 kB]
Get:183 http://172.17.0.1/private bookworm-staging/main armhf mafft armhf 7.487-1 [710 kB]
Get:184 http://172.17.0.1/private bookworm-staging/main armhf muscle armhf 1:3.8.1551-2 [189 kB]
Get:185 http://172.17.0.1/private bookworm-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB]
Get:186 http://172.17.0.1/private bookworm-staging/main armhf ncbi-blast+ armhf 2.11.0+ds-1 [9360 kB]
Get:187 http://172.17.0.1/private bookworm-staging/main armhf phylip armhf 1:3.697+dfsg-2 [683 kB]
Get:188 http://172.17.0.1/private bookworm-staging/main armhf prank armhf 0.0.170427+dfsg-3 [298 kB]
Get:189 http://172.17.0.1/private bookworm-staging/main armhf preview-latex-style all 12.2-1 [201 kB]
Get:190 http://172.17.0.1/private bookworm-staging/main armhf probcons armhf 1.12-14 [100 kB]
Get:191 http://172.17.0.1/private bookworm-staging/main armhf python-matplotlib-data all 3.3.4-2 [4154 kB]
Get:192 http://172.17.0.1/private bookworm-staging/main armhf python3-all armhf 3.9.2-3 [1056 B]
Get:193 http://172.17.0.1/private bookworm-staging/main armhf python3.9-dev armhf 3.9.7-4+rpi1 [501 kB]
Get:194 http://172.17.0.1/private bookworm-staging/main armhf python3-dev armhf 3.9.2-3 [24.8 kB]
Get:195 http://172.17.0.1/private bookworm-staging/main armhf python3-all-dev armhf 3.9.2-3 [1064 B]
Get:196 http://172.17.0.1/private bookworm-staging/main armhf python3-six all 1.16.0-2 [17.5 kB]
Get:197 http://172.17.0.1/private bookworm-staging/main armhf python3-cycler all 0.10.0-3 [8084 B]
Get:198 http://172.17.0.1/private bookworm-staging/main armhf python3-dateutil all 2.8.1-6 [79.2 kB]
Get:199 http://172.17.0.1/private bookworm-staging/main armhf python3-decorator all 4.4.2-2 [15.8 kB]
Get:200 http://172.17.0.1/private bookworm-staging/main armhf python3-isodate all 0.6.0-2 [25.0 kB]
Get:201 http://172.17.0.1/private bookworm-staging/main armhf python3-kiwisolver armhf 1.3.2-1 [45.8 kB]
Get:202 http://172.17.0.1/private bookworm-staging/main armhf python3-linecache2 all 1.0.0-4 [12.8 kB]
Get:203 http://172.17.0.1/private bookworm-staging/main armhf python3-pyparsing all 2.4.7-1 [109 kB]
Get:204 http://172.17.0.1/private bookworm-staging/main armhf python3-pkg-resources all 58.2.0-1 [192 kB]
Get:205 http://172.17.0.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.19.5-1 [2930 kB]
Get:206 http://172.17.0.1/private bookworm-staging/main armhf python3-pil armhf 8.3.2-1 [419 kB]
Get:207 http://172.17.0.1/private bookworm-staging/main armhf python3-matplotlib armhf 3.3.4-2 [6035 kB]
Get:208 http://172.17.0.1/private bookworm-staging/main armhf python3-msgpack armhf 1.0.2-2 [64.2 kB]
Get:209 http://172.17.0.1/private bookworm-staging/main armhf python3-mmtf all 1.1.2-3 [16.8 kB]
Get:210 http://172.17.0.1/private bookworm-staging/main armhf python3-mysqldb armhf 1.4.4-2+b1 [54.3 kB]
Get:211 http://172.17.0.1/private bookworm-staging/main armhf python3-networkx all 2.5+ds-2 [900 kB]
Get:212 http://172.17.0.1/private bookworm-staging/main armhf python3-psycopg2 armhf 2.8.6-2 [107 kB]
Get:213 http://172.17.0.1/private bookworm-staging/main armhf python3-pygments all 2.7.1+dfsg-2.1 [657 kB]
Get:214 http://172.17.0.1/private bookworm-staging/main armhf python3-rdflib all 5.0.0-1.1 [196 kB]
Get:215 http://172.17.0.1/private bookworm-staging/main armhf python3-renderpm armhf 3.5.59-2 [66.9 kB]
Get:216 http://172.17.0.1/private bookworm-staging/main armhf python3-reportlab-accel armhf 3.5.59-2 [37.3 kB]
Get:217 http://172.17.0.1/private bookworm-staging/main armhf python3-reportlab all 3.5.59-2 [575 kB]
Get:218 http://172.17.0.1/private bookworm-staging/main armhf python3-scipy armhf 1.6.0-2 [11.1 MB]
Get:219 http://172.17.0.1/private bookworm-staging/main armhf python3-setuptools all 58.2.0-1 [396 kB]
Get:220 http://172.17.0.1/private bookworm-staging/main armhf python3-traceback2 all 1.4.0-6 [16.6 kB]
Get:221 http://172.17.0.1/private bookworm-staging/main armhf python3-unittest2 all 1.1.0-7 [75.5 kB]
Get:222 http://172.17.0.1/private bookworm-staging/main armhf samtools armhf 1.13-2 [525 kB]
Get:223 http://172.17.0.1/private bookworm-staging/main armhf t-coffee armhf 13.41.0.28bdc39+dfsg-4 [780 kB]
Get:224 http://172.17.0.1/private bookworm-staging/main armhf texlive-fonts-recommended all 2021.20210921-1 [5004 kB]
Get:225 http://172.17.0.1/private bookworm-staging/main armhf texlive-latex-base all 2021.20210921-1 [1150 kB]
Get:226 http://172.17.0.1/private bookworm-staging/main armhf texlive-latex-recommended all 2021.20210921-1 [14.4 MB]
Get:227 http://172.17.0.1/private bookworm-staging/main armhf texlive-pictures all 2021.20210921-1 [8775 kB]
Get:228 http://172.17.0.1/private bookworm-staging/main armhf texlive-latex-extra all 2021.20210921-1 [14.5 MB]
Get:229 http://172.17.0.1/private bookworm-staging/main armhf wise-data all 2.4.1-23 [78.2 kB]
Get:230 http://172.17.0.1/private bookworm-staging/main armhf wise armhf 2.4.1-23 [704 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 257 MB in 38s (6677 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12477 files and directories currently installed.)
Preparing to unpack .../bsdextrautils_2.37.2-3_armhf.deb ...
Unpacking bsdextrautils (2.37.2-3) ...
Preparing to unpack .../libasan6_11.2.0-9+rpi1_armhf.deb ...
Unpacking libasan6:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libubsan1_11.2.0-9+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libgomp1_11.2.0-9+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../gcc-11-base_11.2.0-9+rpi1_armhf.deb ...
Unpacking gcc-11-base:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Setting up gcc-11-base:armhf (11.2.0-9+rpi1) ...
(Reading database ... 12508 files and directories currently installed.)
Preparing to unpack .../libgcc-s1_11.2.0-9+rpi1_armhf.deb ...
Unpacking libgcc-s1:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Setting up libgcc-s1:armhf (11.2.0-9+rpi1) ...
(Reading database ... 12508 files and directories currently installed.)
Preparing to unpack .../libcc1-0_11.2.0-9+rpi1_armhf.deb ...
Unpacking libcc1-0:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libatomic1_11.2.0-9+rpi1_armhf.deb ...
Unpacking libatomic1:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libstdc++6_11.2.0-9+rpi1_armhf.deb ...
Unpacking libstdc++6:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Setting up libstdc++6:armhf (11.2.0-9+rpi1) ...
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12508 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../01-groff-base_1.22.4-7_armhf.deb ...
Unpacking groff-base (1.22.4-7) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../02-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../03-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../04-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../05-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package flex.
Preparing to unpack .../06-flex_2.6.4-8_armhf.deb ...
Unpacking flex (2.6.4-8) ...
Selecting previously unselected package poppler-data.
Preparing to unpack .../07-poppler-data_0.4.11-1_all.deb ...
Unpacking poppler-data (0.4.11-1) ...
Selecting previously unselected package libpython3.9-minimal:armhf.
Preparing to unpack .../08-libpython3.9-minimal_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../09-libexpat1_2.4.1-2_armhf.deb ...
Unpacking libexpat1:armhf (2.4.1-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../10-python3.9-minimal_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9-minimal (3.9.7-4+rpi1) ...
Setting up libpython3.9-minimal:armhf (3.9.7-4+rpi1) ...
Setting up libexpat1:armhf (2.4.1-2) ...
Setting up python3.9-minimal (3.9.7-4+rpi1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 14045 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.deb ...
Unpacking python3-minimal (3.9.2-3) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package mailcap.
Preparing to unpack .../2-mailcap_3.70_all.deb ...
Unpacking mailcap (3.70) ...
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 libffi8:armhf.
Preparing to unpack .../4-libffi8_3.4.2-3_armhf.deb ...
Unpacking libffi8:armhf (3.4.2-3) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../5-libmpdec3_2.5.1-2+rpi1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-2+rpi1) ...
Selecting previously unselected package libpython3.9-stdlib:armhf.
Preparing to unpack .../6-libpython3.9-stdlib_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package python3.9.
Preparing to unpack .../7-python3.9_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9 (3.9.7-4+rpi1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../8-libpython3-stdlib_3.9.2-3_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.9.2-3) ...
Setting up python3-minimal (3.9.2-3) ...
Selecting previously unselected package python3.
(Reading database ... 14472 files and directories currently installed.)
Preparing to unpack .../000-python3_3.9.2-3_armhf.deb ...
Unpacking python3 (3.9.2-3) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../001-sensible-utils_0.0.17_all.deb ...
Unpacking sensible-utils (0.0.17) ...
Selecting previously unselected package ucf.
Preparing to unpack .../002-ucf_3.0043_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043) ...
Selecting previously unselected package tex-common.
Preparing to unpack .../003-tex-common_6.17_all.deb ...
Unpacking tex-common (6.17) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../004-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../005-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../006-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../007-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../008-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../009-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../010-automake_1%3a1.16.5-1_all.deb ...
Unpacking automake (1:1.16.5-1) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../011-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package bwa.
Preparing to unpack .../012-bwa_0.7.17-6_armhf.deb ...
Unpacking bwa (0.7.17-6) ...
Selecting previously unselected package libargtable2-0.
Preparing to unpack .../013-libargtable2-0_13-1.1_armhf.deb ...
Unpacking libargtable2-0 (13-1.1) ...
Selecting previously unselected package clustalo.
Preparing to unpack .../014-clustalo_1.2.4-7_armhf.deb ...
Unpacking clustalo (1.2.4-7) ...
Selecting previously unselected package clustalw.
Preparing to unpack .../015-clustalw_2.1+lgpl-7_armhf.deb ...
Unpacking clustalw (2.1+lgpl-7) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../016-libdebhelper-perl_13.5.2_all.deb ...
Unpacking libdebhelper-perl (13.5.2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../017-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../018-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../019-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 .../020-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../021-libfile-stripnondeterminism-perl_1.12.0-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.12.0-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../022-dh-strip-nondeterminism_1.12.0-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.12.0-2) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../023-libelf1_0.185-2_armhf.deb ...
Unpacking libelf1:armhf (0.185-2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../024-dwz_0.14-1_armhf.deb ...
Unpacking dwz (0.14-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../025-libicu67_67.1-7_armhf.deb ...
Unpacking libicu67:armhf (67.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../026-libxml2_2.9.12+dfsg-5_armhf.deb ...
Unpacking libxml2:armhf (2.9.12+dfsg-5) ...
Selecting previously unselected package gettext.
Preparing to unpack .../027-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../028-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../029-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../030-debhelper_13.5.2_all.deb ...
Unpacking debhelper (13.5.2) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../031-python3-lib2to3_3.9.7-1_all.deb ...
Unpacking python3-lib2to3 (3.9.7-1) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../032-python3-distutils_3.9.7-1_all.deb ...
Unpacking python3-distutils (3.9.7-1) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../033-dh-python_5.20211016.1_all.deb ...
Unpacking dh-python (5.20211016.1) ...
Selecting previously unselected package dialign.
Preparing to unpack .../034-dialign_2.2.1-11_armhf.deb ...
Unpacking dialign (2.2.1-11) ...
Selecting previously unselected package libboost-iostreams1.74.0:armhf.
Preparing to unpack .../035-libboost-iostreams1.74.0_1.74.0-9_armhf.deb ...
Unpacking libboost-iostreams1.74.0:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-program-options1.74.0:armhf.
Preparing to unpack .../036-libboost-program-options1.74.0_1.74.0-9_armhf.deb ...
Unpacking libboost-program-options1.74.0:armhf (1.74.0-9) ...
Selecting previously unselected package libcifpp1.
Preparing to unpack .../037-libcifpp1_1.0.1-3_armhf.deb ...
Unpacking libcifpp1 (1.0.1-3) ...
Selecting previously unselected package dssp.
Preparing to unpack .../038-dssp_4.0.0-2_armhf.deb ...
Unpacking dssp (4.0.0-2) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../039-libbrotli1_1.0.9-2+b1_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b1) ...
Selecting previously unselected package libpng16-16:armhf.
Preparing to unpack .../040-libpng16-16_1.6.37-3_armhf.deb ...
Unpacking libpng16-16:armhf (1.6.37-3) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../041-libfreetype6_2.11.0+dfsg-1_armhf.deb ...
Unpacking libfreetype6:armhf (2.11.0+dfsg-1) ...
Selecting previously unselected package ttf-bitstream-vera.
Preparing to unpack .../042-ttf-bitstream-vera_1.10-8.1_all.deb ...
Unpacking ttf-bitstream-vera (1.10-8.1) ...
Selecting previously unselected package fonts-urw-base35.
Preparing to unpack .../043-fonts-urw-base35_20200910-1_all.deb ...
Unpacking fonts-urw-base35 (20200910-1) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../044-fontconfig-config_2.13.1-4.2_all.deb ...
Unpacking fontconfig-config (2.13.1-4.2) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../045-libfontconfig1_2.13.1-4.2_armhf.deb ...
Unpacking libfontconfig1:armhf (2.13.1-4.2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../046-libjpeg62-turbo_1%3a2.0.6-4_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.0.6-4) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../047-libdeflate0_1.8-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.8-1) ...
Selecting previously unselected package libjbig0:armhf.
Preparing to unpack .../048-libjbig0_2.1-3.1+b2_armhf.deb ...
Unpacking libjbig0:armhf (2.1-3.1+b2) ...
Selecting previously unselected package libwebp6:armhf.
Preparing to unpack .../049-libwebp6_0.6.1-2.1_armhf.deb ...
Unpacking libwebp6:armhf (0.6.1-2.1) ...
Selecting previously unselected package libtiff5:armhf.
Preparing to unpack .../050-libtiff5_4.3.0-2_armhf.deb ...
Unpacking libtiff5:armhf (4.3.0-2) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../051-libxau6_1%3a1.0.9-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.9-1) ...
Selecting previously unselected package libmd0:armhf.
Preparing to unpack .../052-libmd0_1.0.4-1_armhf.deb ...
Unpacking libmd0:armhf (1.0.4-1) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../053-libbsd0_0.11.3-1_armhf.deb ...
Unpacking libbsd0:armhf (0.11.3-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../054-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 .../055-libxcb1_1.14-3_armhf.deb ...
Unpacking libxcb1:armhf (1.14-3) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../056-libx11-data_2%3a1.7.2-2_all.deb ...
Unpacking libx11-data (2:1.7.2-2) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../057-libx11-6_2%3a1.7.2-2_armhf.deb ...
Unpacking libx11-6:armhf (2:1.7.2-2) ...
Selecting previously unselected package libxpm4:armhf.
Preparing to unpack .../058-libxpm4_1%3a3.5.12-1_armhf.deb ...
Unpacking libxpm4:armhf (1:3.5.12-1) ...
Selecting previously unselected package libgd3:armhf.
Preparing to unpack .../059-libgd3_2.3.0-2_armhf.deb ...
Unpacking libgd3:armhf (2.3.0-2) ...
Selecting previously unselected package libhpdf-2.3.0:armhf.
Preparing to unpack .../060-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 .../061-mysql-common_5.8+1.0.7_all.deb ...
Unpacking mysql-common (5.8+1.0.7) ...
Selecting previously unselected package mariadb-common.
Preparing to unpack .../062-mariadb-common_1%3a10.5.12-1_all.deb ...
Unpacking mariadb-common (1:10.5.12-1) ...
Selecting previously unselected package libmariadb3:armhf.
Preparing to unpack .../063-libmariadb3_1%3a10.5.12-1_armhf.deb ...
Unpacking libmariadb3:armhf (1:10.5.12-1) ...
Selecting previously unselected package libpq5:armhf.
Preparing to unpack .../064-libpq5_14.0-1_armhf.deb ...
Unpacking libpq5:armhf (14.0-1) ...
Selecting previously unselected package emboss-lib.
Preparing to unpack .../065-emboss-lib_6.6.0+dfsg-9_armhf.deb ...
Unpacking emboss-lib (6.6.0+dfsg-9) ...
Selecting previously unselected package emboss-data.
Preparing to unpack .../066-emboss-data_6.6.0+dfsg-9_all.deb ...
Unpacking emboss-data (6.6.0+dfsg-9) ...
Selecting previously unselected package emboss.
Preparing to unpack .../067-emboss_6.6.0+dfsg-9_armhf.deb ...
Unpacking emboss (6.6.0+dfsg-9) ...
Selecting previously unselected package fasttree.
Preparing to unpack .../068-fasttree_2.1.11-2_armhf.deb ...
Unpacking fasttree (2.1.11-2) ...
Selecting previously unselected package fonts-lmodern.
Preparing to unpack .../069-fonts-lmodern_2.004.5-6.1_all.deb ...
Unpacking fonts-lmodern (2.004.5-6.1) ...
Selecting previously unselected package fonts-lyx.
Preparing to unpack .../070-fonts-lyx_2.3.6-1_all.deb ...
Unpacking fonts-lyx (2.3.6-1) ...
Selecting previously unselected package libgs9-common.
Preparing to unpack .../071-libgs9-common_9.54.0~dfsg-5_all.deb ...
Unpacking libgs9-common (9.54.0~dfsg-5) ...
Selecting previously unselected package libavahi-common-data:armhf.
Preparing to unpack .../072-libavahi-common-data_0.8-5_armhf.deb ...
Unpacking libavahi-common-data:armhf (0.8-5) ...
Selecting previously unselected package libavahi-common3:armhf.
Preparing to unpack .../073-libavahi-common3_0.8-5_armhf.deb ...
Unpacking libavahi-common3:armhf (0.8-5) ...
Selecting previously unselected package libdbus-1-3:armhf.
Preparing to unpack .../074-libdbus-1-3_1.12.20-2_armhf.deb ...
Unpacking libdbus-1-3:armhf (1.12.20-2) ...
Selecting previously unselected package libavahi-client3:armhf.
Preparing to unpack .../075-libavahi-client3_0.8-5_armhf.deb ...
Unpacking libavahi-client3:armhf (0.8-5) ...
Selecting previously unselected package libcups2:armhf.
Preparing to unpack .../076-libcups2_2.3.3op2-7_armhf.deb ...
Unpacking libcups2:armhf (2.3.3op2-7) ...
Selecting previously unselected package libidn12:armhf.
Preparing to unpack .../077-libidn12_1.38-3_armhf.deb ...
Unpacking libidn12:armhf (1.38-3) ...
Selecting previously unselected package libijs-0.35:armhf.
Preparing to unpack .../078-libijs-0.35_0.35-15_armhf.deb ...
Unpacking libijs-0.35:armhf (0.35-15) ...
Selecting previously unselected package libjbig2dec0:armhf.
Preparing to unpack .../079-libjbig2dec0_0.19-3_armhf.deb ...
Unpacking libjbig2dec0:armhf (0.19-3) ...
Selecting previously unselected package liblcms2-2:armhf.
Preparing to unpack .../080-liblcms2-2_2.12~rc1-2_armhf.deb ...
Unpacking liblcms2-2:armhf (2.12~rc1-2) ...
Selecting previously unselected package libopenjp2-7:armhf.
Preparing to unpack .../081-libopenjp2-7_2.4.0-3_armhf.deb ...
Unpacking libopenjp2-7:armhf (2.4.0-3) ...
Selecting previously unselected package libpaper1:armhf.
Preparing to unpack .../082-libpaper1_1.1.28_armhf.deb ...
Unpacking libpaper1:armhf (1.1.28) ...
Selecting previously unselected package libgs9:armhf.
Preparing to unpack .../083-libgs9_9.54.0~dfsg-5_armhf.deb ...
Unpacking libgs9:armhf (9.54.0~dfsg-5) ...
Selecting previously unselected package ghostscript.
Preparing to unpack .../084-ghostscript_9.54.0~dfsg-5_armhf.deb ...
Unpacking ghostscript (9.54.0~dfsg-5) ...
Selecting previously unselected package libnetpbm10.
Preparing to unpack .../085-libnetpbm10_2%3a10.0-15.4_armhf.deb ...
Unpacking libnetpbm10 (2:10.0-15.4) ...
Selecting previously unselected package netpbm.
Preparing to unpack .../086-netpbm_2%3a10.0-15.4_armhf.deb ...
Unpacking netpbm (2:10.0-15.4) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../087-libpaper-utils_1.1.28_armhf.deb ...
Unpacking libpaper-utils (1.1.28) ...
Selecting previously unselected package libkpathsea6:armhf.
Preparing to unpack .../088-libkpathsea6_2021.20210626.59705-1_armhf.deb ...
Unpacking libkpathsea6:armhf (2021.20210626.59705-1) ...
Selecting previously unselected package libptexenc1:armhf.
Preparing to unpack .../089-libptexenc1_2021.20210626.59705-1_armhf.deb ...
Unpacking libptexenc1:armhf (2021.20210626.59705-1) ...
Selecting previously unselected package libsynctex2:armhf.
Preparing to unpack .../090-libsynctex2_2021.20210626.59705-1_armhf.deb ...
Unpacking libsynctex2:armhf (2021.20210626.59705-1) ...
Selecting previously unselected package libtexlua53:armhf.
Preparing to unpack .../091-libtexlua53_2021.20210626.59705-1_armhf.deb ...
Unpacking libtexlua53:armhf (2021.20210626.59705-1) ...
Selecting previously unselected package libtexluajit2:armhf.
Preparing to unpack .../092-libtexluajit2_2021.20210626.59705-1_armhf.deb ...
Unpacking libtexluajit2:armhf (2021.20210626.59705-1) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../093-t1utils_1.41-4_armhf.deb ...
Unpacking t1utils (1.41-4) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../094-libpixman-1-0_0.40.0-1_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.40.0-1) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../095-libxcb-render0_1.14-3_armhf.deb ...
Unpacking libxcb-render0:armhf (1.14-3) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../096-libxcb-shm0_1.14-3_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.14-3) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../097-libxext6_2%3a1.3.4-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.4-1) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../098-libxrender1_1%3a0.9.10-1_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../099-libcairo2_1.16.0-5_armhf.deb ...
Unpacking libcairo2:armhf (1.16.0-5) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../100-libgraphite2-3_1.3.14-1_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.14-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../101-libglib2.0-0_2.70.0-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.70.0-1) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../102-libharfbuzz0b_2.7.4-1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (2.7.4-1) ...
Selecting previously unselected package libteckit0:armhf.
Preparing to unpack .../103-libteckit0_2.5.10+ds1-3_armhf.deb ...
Unpacking libteckit0:armhf (2.5.10+ds1-3) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../104-x11-common_1%3a7.7+23_all.deb ...
Unpacking x11-common (1:7.7+23) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../105-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 .../106-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 .../107-libxt6_1%3a1.2.0-1_armhf.deb ...
Unpacking libxt6:armhf (1:1.2.0-1) ...
Selecting previously unselected package libxmu6:armhf.
Preparing to unpack .../108-libxmu6_2%3a1.1.2-2+b3_armhf.deb ...
Unpacking libxmu6:armhf (2:1.1.2-2+b3) ...
Selecting previously unselected package libxaw7:armhf.
Preparing to unpack .../109-libxaw7_2%3a1.0.13-1.1_armhf.deb ...
Unpacking libxaw7:armhf (2:1.0.13-1.1) ...
Selecting previously unselected package libxi6:armhf.
Preparing to unpack .../110-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 .../111-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 .../112-texlive-binaries_2021.20210626.59705-1_armhf.deb ...
Unpacking texlive-binaries (2021.20210626.59705-1) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../113-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 .../114-texlive-base_2021.20210921-1_all.deb ...
Unpacking texlive-base (2021.20210921-1) ...
Selecting previously unselected package hevea.
Preparing to unpack .../115-hevea_2.35-1_armhf.deb ...
Unpacking hevea (2.35-1) ...
Selecting previously unselected package libapache-pom-java.
Preparing to unpack .../116-libapache-pom-java_18-1_all.deb ...
Unpacking libapache-pom-java (18-1) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../117-libblas3_3.10.0-1_armhf.deb ...
Unpacking libblas3:armhf (3.10.0-1) ...
Selecting previously unselected package libcommons-parent-java.
Preparing to unpack .../118-libcommons-parent-java_43-1_all.deb ...
Unpacking libcommons-parent-java (43-1) ...
Selecting previously unselected package libcommons-logging-java.
Preparing to unpack .../119-libcommons-logging-java_1.2-2_all.deb ...
Unpacking libcommons-logging-java (1.2-2) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../120-libnghttp2-14_1.43.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.43.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../121-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../122-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 .../123-libssh2-1_1.10.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-2) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../124-libcurl3-gnutls_7.74.0-1.3_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.74.0-1.3) ...
Selecting previously unselected package libexpat1-dev:armhf.
Preparing to unpack .../125-libexpat1-dev_2.4.1-2_armhf.deb ...
Unpacking libexpat1-dev:armhf (2.4.1-2) ...
Selecting previously unselected package libfontbox-java.
Preparing to unpack .../126-libfontbox-java_1%3a1.8.16-2_all.deb ...
Unpacking libfontbox-java (1:1.8.16-2) ...
Selecting previously unselected package libfribidi0:armhf.
Preparing to unpack .../127-libfribidi0_1.0.8-2_armhf.deb ...
Unpacking libfribidi0:armhf (1.0.8-2) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../128-libgfortran5_11.2.0-9+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (11.2.0-9+rpi1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../129-libhtscodecs2_1.1.1-3_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.1.1-3) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../130-libhts3_1.13+ds-2_armhf.deb ...
Unpacking libhts3:armhf (1.13+ds-2) ...
Selecting previously unselected package libimagequant0:armhf.
Preparing to unpack .../131-libimagequant0_2.12.2-1.1_armhf.deb ...
Unpacking libimagequant0:armhf (2.12.2-1.1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../132-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ...
Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../133-libjs-jquery-ui_1.12.1+dfsg-8_all.deb ...
Unpacking libjs-jquery-ui (1.12.1+dfsg-8) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../134-libjs-underscore_1.9.1~dfsg-4_all.deb ...
Unpacking libjs-underscore (1.9.1~dfsg-4) ...
Selecting previously unselected package libjs-sphinxdoc.
Preparing to unpack .../135-libjs-sphinxdoc_4.2.0-4_all.deb ...
Unpacking libjs-sphinxdoc (4.2.0-4) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../136-liblapack3_3.10.0-1_armhf.deb ...
Unpacking liblapack3:armhf (3.10.0-1) ...
Selecting previously unselected package liblbfgsb0:armhf.
Preparing to unpack .../137-liblbfgsb0_3.0+dfsg.3-9_armhf.deb ...
Unpacking liblbfgsb0:armhf (3.0+dfsg.3-9) ...
Selecting previously unselected package liblmdb0:armhf.
Preparing to unpack .../138-liblmdb0_0.9.24-1_armhf.deb ...
Unpacking liblmdb0:armhf (0.9.24-1) ...
Selecting previously unselected package libmbedcrypto3:armhf.
Preparing to unpack .../139-libmbedcrypto3_2.16.9-0.1_armhf.deb ...
Unpacking libmbedcrypto3:armhf (2.16.9-0.1) ...
Selecting previously unselected package libmbedx509-0:armhf.
Preparing to unpack .../140-libmbedx509-0_2.16.9-0.1_armhf.deb ...
Unpacking libmbedx509-0:armhf (2.16.9-0.1) ...
Selecting previously unselected package libmbedtls12:armhf.
Preparing to unpack .../141-libmbedtls12_2.16.9-0.1_armhf.deb ...
Unpacking libmbedtls12:armhf (2.16.9-0.1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../142-libncurses6_6.2+20201114-4_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-4) ...
Selecting previously unselected package libpdfbox-java.
Preparing to unpack .../143-libpdfbox-java_1%3a1.8.16-2_all.deb ...
Unpacking libpdfbox-java (1:1.8.16-2) ...
Selecting previously unselected package libpython3.9:armhf.
Preparing to unpack .../144-libpython3.9_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../145-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libpython3.9-dev:armhf.
Preparing to unpack .../146-libpython3.9-dev_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-dev:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package libpython3-dev:armhf.
Preparing to unpack .../147-libpython3-dev_3.9.2-3_armhf.deb ...
Unpacking libpython3-dev:armhf (3.9.2-3) ...
Selecting previously unselected package libpython3-all-dev:armhf.
Preparing to unpack .../148-libpython3-all-dev_3.9.2-3_armhf.deb ...
Unpacking libpython3-all-dev:armhf (3.9.2-3) ...
Selecting previously unselected package libraqm0:armhf.
Preparing to unpack .../149-libraqm0_0.7.0-4_armhf.deb ...
Unpacking libraqm0:armhf (0.7.0-4) ...
Selecting previously unselected package libwebpdemux2:armhf.
Preparing to unpack .../150-libwebpdemux2_0.6.1-2.1_armhf.deb ...
Unpacking libwebpdemux2:armhf (0.6.1-2.1) ...
Selecting previously unselected package libwebpmux3:armhf.
Preparing to unpack .../151-libwebpmux3_0.6.1-2.1_armhf.deb ...
Unpacking libwebpmux3:armhf (0.6.1-2.1) ...
Selecting previously unselected package mafft.
Preparing to unpack .../152-mafft_7.487-1_armhf.deb ...
Unpacking mafft (7.487-1) ...
Selecting previously unselected package muscle.
Preparing to unpack .../153-muscle_1%3a3.8.1551-2_armhf.deb ...
Unpacking muscle (1:3.8.1551-2) ...
Selecting previously unselected package ncbi-data.
Preparing to unpack .../154-ncbi-data_6.1.20170106+dfsg1-9_all.deb ...
Unpacking ncbi-data (6.1.20170106+dfsg1-9) ...
Selecting previously unselected package ncbi-blast+.
Preparing to unpack .../155-ncbi-blast+_2.11.0+ds-1_armhf.deb ...
Unpacking ncbi-blast+ (2.11.0+ds-1) ...
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_3.3.4-2_all.deb ...
Unpacking python-matplotlib-data (3.3.4-2) ...
Selecting previously unselected package python3-all.
Preparing to unpack .../161-python3-all_3.9.2-3_armhf.deb ...
Unpacking python3-all (3.9.2-3) ...
Selecting previously unselected package python3.9-dev.
Preparing to unpack .../162-python3.9-dev_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9-dev (3.9.7-4+rpi1) ...
Selecting previously unselected package python3-dev.
Preparing to unpack .../163-python3-dev_3.9.2-3_armhf.deb ...
Unpacking python3-dev (3.9.2-3) ...
Selecting previously unselected package python3-all-dev.
Preparing to unpack .../164-python3-all-dev_3.9.2-3_armhf.deb ...
Unpacking python3-all-dev (3.9.2-3) ...
Selecting previously unselected package python3-six.
Preparing to unpack .../165-python3-six_1.16.0-2_all.deb ...
Unpacking python3-six (1.16.0-2) ...
Selecting previously unselected package python3-cycler.
Preparing to unpack .../166-python3-cycler_0.10.0-3_all.deb ...
Unpacking python3-cycler (0.10.0-3) ...
Selecting previously unselected package python3-dateutil.
Preparing to unpack .../167-python3-dateutil_2.8.1-6_all.deb ...
Unpacking python3-dateutil (2.8.1-6) ...
Selecting previously unselected package python3-decorator.
Preparing to unpack .../168-python3-decorator_4.4.2-2_all.deb ...
Unpacking python3-decorator (4.4.2-2) ...
Selecting previously unselected package python3-isodate.
Preparing to unpack .../169-python3-isodate_0.6.0-2_all.deb ...
Unpacking python3-isodate (0.6.0-2) ...
Selecting previously unselected package python3-kiwisolver.
Preparing to unpack .../170-python3-kiwisolver_1.3.2-1_armhf.deb ...
Unpacking python3-kiwisolver (1.3.2-1) ...
Selecting previously unselected package python3-linecache2.
Preparing to unpack .../171-python3-linecache2_1.0.0-4_all.deb ...
Unpacking python3-linecache2 (1.0.0-4) ...
Selecting previously unselected package python3-pyparsing.
Preparing to unpack .../172-python3-pyparsing_2.4.7-1_all.deb ...
Unpacking python3-pyparsing (2.4.7-1) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../173-python3-pkg-resources_58.2.0-1_all.deb ...
Unpacking python3-pkg-resources (58.2.0-1) ...
Selecting previously unselected package python3-numpy.
Preparing to unpack .../174-python3-numpy_1%3a1.19.5-1_armhf.deb ...
Unpacking python3-numpy (1:1.19.5-1) ...
Selecting previously unselected package python3-pil:armhf.
Preparing to unpack .../175-python3-pil_8.3.2-1_armhf.deb ...
Unpacking python3-pil:armhf (8.3.2-1) ...
Selecting previously unselected package python3-matplotlib.
Preparing to unpack .../176-python3-matplotlib_3.3.4-2_armhf.deb ...
Unpacking python3-matplotlib (3.3.4-2) ...
Selecting previously unselected package python3-msgpack.
Preparing to unpack .../177-python3-msgpack_1.0.2-2_armhf.deb ...
Unpacking python3-msgpack (1.0.2-2) ...
Selecting previously unselected package python3-mmtf.
Preparing to unpack .../178-python3-mmtf_1.1.2-3_all.deb ...
Unpacking python3-mmtf (1.1.2-3) ...
Selecting previously unselected package python3-mysqldb.
Preparing to unpack .../179-python3-mysqldb_1.4.4-2+b1_armhf.deb ...
Unpacking python3-mysqldb (1.4.4-2+b1) ...
Selecting previously unselected package python3-networkx.
Preparing to unpack .../180-python3-networkx_2.5+ds-2_all.deb ...
Unpacking python3-networkx (2.5+ds-2) ...
Selecting previously unselected package python3-psycopg2.
Preparing to unpack .../181-python3-psycopg2_2.8.6-2_armhf.deb ...
Unpacking python3-psycopg2 (2.8.6-2) ...
Selecting previously unselected package python3-pygments.
Preparing to unpack .../182-python3-pygments_2.7.1+dfsg-2.1_all.deb ...
Unpacking python3-pygments (2.7.1+dfsg-2.1) ...
Selecting previously unselected package python3-rdflib.
Preparing to unpack .../183-python3-rdflib_5.0.0-1.1_all.deb ...
Unpacking python3-rdflib (5.0.0-1.1) ...
Selecting previously unselected package python3-renderpm:armhf.
Preparing to unpack .../184-python3-renderpm_3.5.59-2_armhf.deb ...
Unpacking python3-renderpm:armhf (3.5.59-2) ...
Selecting previously unselected package python3-reportlab-accel:armhf.
Preparing to unpack .../185-python3-reportlab-accel_3.5.59-2_armhf.deb ...
Unpacking python3-reportlab-accel:armhf (3.5.59-2) ...
Selecting previously unselected package python3-reportlab.
Preparing to unpack .../186-python3-reportlab_3.5.59-2_all.deb ...
Unpacking python3-reportlab (3.5.59-2) ...
Selecting previously unselected package python3-scipy.
Preparing to unpack .../187-python3-scipy_1.6.0-2_armhf.deb ...
Unpacking python3-scipy (1.6.0-2) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../188-python3-setuptools_58.2.0-1_all.deb ...
Unpacking python3-setuptools (58.2.0-1) ...
Selecting previously unselected package python3-traceback2.
Preparing to unpack .../189-python3-traceback2_1.4.0-6_all.deb ...
Unpacking python3-traceback2 (1.4.0-6) ...
Selecting previously unselected package python3-unittest2.
Preparing to unpack .../190-python3-unittest2_1.1.0-7_all.deb ...
Unpacking python3-unittest2 (1.1.0-7) ...
Selecting previously unselected package samtools.
Preparing to unpack .../191-samtools_1.13-2_armhf.deb ...
Unpacking samtools (1.13-2) ...
Selecting previously unselected package t-coffee.
Preparing to unpack .../192-t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb ...
Unpacking t-coffee (13.41.0.28bdc39+dfsg-4) ...
Selecting previously unselected package texlive-fonts-recommended.
Preparing to unpack .../193-texlive-fonts-recommended_2021.20210921-1_all.deb ...
Unpacking texlive-fonts-recommended (2021.20210921-1) ...
Selecting previously unselected package texlive-latex-base.
Preparing to unpack .../194-texlive-latex-base_2021.20210921-1_all.deb ...
Unpacking texlive-latex-base (2021.20210921-1) ...
Selecting previously unselected package texlive-latex-recommended.
Preparing to unpack .../195-texlive-latex-recommended_2021.20210921-1_all.deb ...
Unpacking texlive-latex-recommended (2021.20210921-1) ...
Selecting previously unselected package texlive-pictures.
Preparing to unpack .../196-texlive-pictures_2021.20210921-1_all.deb ...
Unpacking texlive-pictures (2021.20210921-1) ...
Selecting previously unselected package texlive-latex-extra.
Preparing to unpack .../197-texlive-latex-extra_2021.20210921-1_all.deb ...
Unpacking texlive-latex-extra (2021.20210921-1) ...
Selecting previously unselected package wise-data.
Preparing to unpack .../198-wise-data_2.4.1-23_all.deb ...
Unpacking wise-data (2.4.1-23) ...
Selecting previously unselected package wise.
Preparing to unpack .../199-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 .../200-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.1.1-3) ...
Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up liblmdb0:armhf (0.9.24-1) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up liblcms2-2:armhf (2.12~rc1-2) ...
Setting up ncbi-data (6.1.20170106+dfsg1-9) ...
Setting up libpixman-1-0:armhf (0.40.0-1) ...
Setting up mysql-common (5.8+1.0.7) ...
update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up ttf-bitstream-vera (1.10-8.1) ...
Setting up bsdextrautils (2.37.2-3) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up probcons (1.12-14) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libtexlua53:armhf (2021.20210626.59705-1) ...
Setting up mafft (7.487-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up bwa (0.7.17-6) ...
Setting up libboost-iostreams1.74.0:armhf (1.74.0-9) ...
Setting up libboost-program-options1.74.0:armhf (1.74.0-9) ...
Setting up fonts-lyx (2.3.6-1) ...
Setting up libijs-0.35:armhf (0.35-15) ...
Setting up libtexluajit2:armhf (2021.20210626.59705-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libfontbox-java (1:1.8.16-2) ...
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 (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libpq5:armhf (14.0-1) ...
Setting up libdeflate0:armhf (1.8-1) ...
Setting up gettext-base (0.21-4) ...
Setting up libzzip-0-13:armhf (0.13.72+dfsg.1-1.1) ...
Setting up file (1:5.39-3) ...
Setting up libnetpbm10 (2:10.0-15.4) ...
Setting up fonts-urw-base35 (20200910-1) ...
Setting up libgomp1:armhf (11.2.0-9+rpi1) ...
Setting up muscle (1:3.8.1551-2) ...
Setting up emboss-data (6.6.0+dfsg-9) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libasan6:armhf (11.2.0-9+rpi1) ...
Setting up t-coffee (13.41.0.28bdc39+dfsg-4) ...
Setting up poppler-data (0.4.11-1) ...
Setting up mariadb-common (1:10.5.12-1) ...
update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.10.0-1) ...
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 (2.4.1-2) ...
Setting up libjpeg62-turbo:armhf (1:2.0.6-4) ...
Setting up libx11-data (2:1.7.2-2) ...
Setting up libjbig2dec0:armhf (0.19-3) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libteckit0:armhf (2.5.10+ds1-3) ...
Setting up libapache-pom-java (18-1) ...
Setting up libavahi-common-data:armhf (0.8-5) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up libdbus-1-3:armhf (1.12.20-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libfribidi0:armhf (1.0.8-2) ...
Setting up t1utils (1.41-4) ...
Setting up libimagequant0:armhf (2.12.2-1.1) ...
Setting up libpng16-16:armhf (1.6.37-3) ...
Setting up libatomic1:armhf (11.2.0-9+rpi1) ...
Setting up libidn12:armhf (1.38-3) ...
Setting up autopoint (0.21-4) ...
Setting up libwebp6:armhf (0.6.1-2.1) ...
Setting up libmariadb3:armhf (1:10.5.12-1) ...
Setting up wise-data (2.4.1-23) ...
Setting up libkpathsea6:armhf (2021.20210626.59705-1) ...
Setting up libgfortran5:armhf (11.2.0-9+rpi1) ...
Setting up libubsan1:armhf (11.2.0-9+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libcifpp1 (1.0.1-3) ...
Setting up libffi8:armhf (3.4.2-3) ...
Setting up libmd0:armhf (1.0.4-1) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up clustalw (2.1+lgpl-7) ...
Setting up fonts-lmodern (2.004.5-6.1) ...
Setting up libmbedcrypto3:armhf (2.16.9-0.1) ...
Setting up libopenjp2-7:armhf (2.4.0-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up fasttree (2.1.11-2) ...
Setting up libtiff5:armhf (4.3.0-2) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Setting up python-matplotlib-data (3.3.4-2) ...
Setting up libwebpmux3:armhf (0.6.1-2.1) ...
Setting up libbsd0:armhf (0.11.3-1) ...
Setting up mailcap (3.70) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up dialign (2.2.1-11) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
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 libcc1-0:armhf (11.2.0-9+rpi1) ...
Setting up libsynctex2:armhf (2021.20210626.59705-1) ...
Setting up libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-3) ...
Setting up prank (0.0.170427+dfsg-3) ...
Setting up libargtable2-0 (13-1.1) ...
Setting up libjs-underscore (1.9.1~dfsg-4) ...
Setting up libgs9-common (9.54.0~dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-2) ...
Setting up libice6:armhf (2:1.0.10-1) ...
Setting up libhpdf-2.3.0:armhf (2.3.0+dfsg-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.10.0-1) ...
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 (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up libpdfbox-java (1:1.8.16-2) ...
Setting up mime-support (3.66) ...
Setting up libtool (2.4.6-15) ...
Setting up libxcb-render0:armhf (1.14-3) ...
Setting up libmbedx509-0:armhf (2.16.9-0.1) ...
Setting up libglib2.0-0:armhf (2.70.0-1) ...
No schema files found: doing nothing.
Setting up wise (2.4.1-23) ...
Setting up libwebpdemux2:armhf (0.6.1-2.1) ...
Setting up libcommons-parent-java (43-1) ...
Setting up libmbedtls12:armhf (2.16.9-0.1) ...
Setting up libavahi-common3:armhf (0.8-5) ...
Setting up libcommons-logging-java (1.2-2) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up libxcb-shm0:armhf (1.14-3) ...
Setting up clustalo (1.2.4-7) ...
Setting up dssp (4.0.0-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libpython3.9:armhf (3.9.7-4+rpi1) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-8) ...
Setting up libptexenc1:armhf (2021.20210626.59705-1) ...
Setting up libfreetype6:armhf (2.11.0+dfsg-1) ...
Setting up ucf (3.0043) ...
Setting up netpbm (2:10.0-15.4) ...
Setting up libjs-sphinxdoc (4.2.0-4) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-2) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up libx11-6:armhf (2:1.7.2-2) ...
Setting up libharfbuzz0b:armhf (2.7.4-1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libavahi-client3:armhf (0.8-5) ...
Setting up python3.9 (3.9.7-4+rpi1) ...
Setting up liblbfgsb0:armhf (3.0+dfsg.3-9) ...
Setting up automake (1:1.16.5-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpaper1:armhf (1.1.28) ...

Creating config file /etc/papersize with new version
Setting up flex (2.6.4-8) ...
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up libxpm4:armhf (1:3.5.12-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up fontconfig-config (2.13.1-4.2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libpython3.9-dev:armhf (3.9.7-4+rpi1) ...
Setting up python3 (3.9.2-3) ...
Setting up libpaper-utils (1.1.28) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.13-2) ...
Setting up ncbi-blast+ (2.11.0+ds-1) ...
Setting up python3-mysqldb (1.4.4-2+b1) ...
Setting up python3-six (1.16.0-2) ...
Setting up dh-autoreconf (20) ...
Setting up tex-common (6.17) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up python3-isodate (0.6.0-2) ...
Setting up python3-decorator (4.4.2-2) ...
Setting up python3-pyparsing (2.4.7-1) ...
Setting up python3-linecache2 (1.0.0-4) ...
Setting up libraqm0:armhf (0.7.0-4) ...
Setting up python3-cycler (0.10.0-3) ...
Setting up python3-reportlab-accel:armhf (3.5.59-2) ...
Setting up python3-kiwisolver (1.3.2-1) ...
Setting up python3-psycopg2 (2.8.6-2) ...
Setting up libxt6:armhf (1:1.2.0-1) ...
Setting up libcups2:armhf (2.3.3op2-7) ...
Setting up python3.9-dev (3.9.7-4+rpi1) ...
Setting up python3-rdflib (5.0.0-1.1) ...
Setting up python3-dateutil (2.8.1-6) ...
Setting up python3-msgpack (1.0.2-2) ...
Setting up libfontconfig1:armhf (2.13.1-4.2) ...
Setting up python3-lib2to3 (3.9.7-1) ...
Setting up python3-pkg-resources (58.2.0-1) ...
Setting up python3-distutils (3.9.7-1) ...
Setting up dh-python (5.20211016.1) ...
Setting up libxmu6:armhf (2:1.1.2-2+b3) ...
Setting up libpython3-dev:armhf (3.9.2-3) ...
Setting up python3-renderpm:armhf (3.5.59-2) ...
Setting up python3-setuptools (58.2.0-1) ...
Setting up libgs9:armhf (9.54.0~dfsg-5) ...
Setting up libxi6:armhf (2:1.8-1) ...
Setting up preview-latex-style (12.2-1) ...
Setting up python3-traceback2 (1.4.0-6) ...
Setting up python3-all (3.9.2-3) ...
Setting up debhelper (13.5.2) ...
Setting up libxaw7:armhf (2:1.0.13-1.1) ...
Setting up ghostscript (9.54.0~dfsg-5) ...
Setting up python3-networkx (2.5+ds-2) ...
Setting up libcairo2:armhf (1.16.0-5) ...
Setting up python3-pil:armhf (8.3.2-1) ...
Setting up python3-pygments (2.7.1+dfsg-2.1) ...
Setting up libpython3-all-dev:armhf (3.9.2-3) ...
Setting up python3-dev (3.9.2-3) ...
Setting up libgd3:armhf (2.3.0-2) ...
Setting up python3-unittest2 (1.1.0-7) ...
update-alternatives: using /usr/bin/python3-unit2 to provide /usr/bin/unit2 (unit2) in auto mode
Setting up python3-numpy (1:1.19.5-1) ...
Setting up python3-reportlab (3.5.59-2) ...
Setting up texlive-binaries (2021.20210626.59705-1) ...
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 emboss-lib (6.6.0+dfsg-9) ...
Setting up texlive-base (2021.20210921-1) ...
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 python3-all-dev (3.9.2-3) ...
Setting up python3-matplotlib (3.3.4-2) ...
Setting up python3-scipy (1.6.0-2) ...
Setting up emboss (6.6.0+dfsg-9) ...
Setting up python3-mmtf (1.1.2-3) ...
Setting up texlive-latex-base (2021.20210921-1) ...
Setting up texlive-latex-recommended (2021.20210921-1) ...
Setting up hevea (2.35-1) ...
Setting up texlive-pictures (2021.20210921-1) ...
Setting up texlive-fonts-recommended (2021.20210921-1) ...
Setting up texlive-latex-extra (2021.20210921-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
Processing triggers for tex-common (6.17) ...
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 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-9+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-1 build-essential_12.9 bwa_0.7.17-6 bzip2_1.0.8-4 clustalo_1.2.4-7 clustalw_2.1+lgpl-7 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-python_5.20211016.1 dh-strip-nondeterminism_1.12.0-2 dialign_2.2.1-11 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dssp_4.0.0-2 dwz_0.14-1 e2fsprogs_1.46.4-1 emboss_6.6.0+dfsg-9 emboss-data_6.6.0+dfsg-9 emboss-lib_6.6.0+dfsg-9 fakeroot_1.25.3-1.1 fasttree_2.1.11-2 file_1:5.39-3 findutils_4.8.0-1 flex_2.6.4-8 fontconfig-config_2.13.1-4.2 fonts-lmodern_2.004.5-6.1 fonts-lyx_2.3.6-1 fonts-urw-base35_20200910-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-9+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_0.21-4 gettext-base_0.21-4 ghostscript_9.54.0~dfsg-5 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hevea_2.35-1 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapache-pom-java_18-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libargtable2-0_13-1.1 libasan6_11.2.0-9+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-9+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libavahi-client3_0.8-5 libavahi-common-data_0.8-5 libavahi-common3_0.8-5 libbinutils_2.37-5+rpi1 libblas3_3.10.0-1 libblkid1_2.37.2-1 libboost-iostreams1.74.0_1.74.0-9 libboost-program-options1.74.0_1.74.0-9 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-9+rpi1 libcifpp1_1.0.1-3 libcom-err2_1.46.4-1 libcommons-logging-java_1.2-2 libcommons-parent-java_43-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcups2_2.3.3op2-7 libcurl3-gnutls_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdbus-1-3_1.12.20-2 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libexpat1_2.4.1-2 libexpat1-dev_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libfontbox-java_1:1.8.16-2 libfontconfig1_2.13.1-4.2 libfreetype6_2.11.0+dfsg-1 libfribidi0_1.0.8-2 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-9+rpi1 libgcrypt20_1.9.4-3 libgd3_2.3.0-2 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgfortran5_11.2.0-9+rpi1 libglib2.0-0_2.70.0-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-9+rpi1 libgpg-error0_1.42-3 libgraphite2-3_1.3.14-1 libgs9_9.54.0~dfsg-5 libgs9-common_9.54.0~dfsg-5 libgssapi-krb5-2_1.18.3-7 libharfbuzz0b_2.7.4-1 libhogweed6_3.7.3-1 libhpdf-2.3.0_2.3.0+dfsg-1 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libice6_2:1.0.10-1 libicu67_67.1-7 libidn12_1.38-3 libidn2-0_2.3.2-2 libijs-0.35_0.35-15 libimagequant0_2.12.2-1.1 libisl23_0.23-1 libjbig0_2.1-3.1+b2 libjbig2dec0_0.19-3 libjpeg62-turbo_1:2.0.6-4 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 libjs-sphinxdoc_4.2.0-4 libjs-underscore_1.9.1~dfsg-4 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkpathsea6_2021.20210626.59705-1 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack3_3.10.0-1 liblbfgsb0_3.0+dfsg.3-9 liblcms2-2_2.12~rc1-2 libldap-2.4-2_2.4.59+dfsg-1 liblmdb0_0.9.24-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmariadb3_1:10.5.12-1 libmbedcrypto3_2.16.9-0.1 libmbedtls12_2.16.9-0.1 libmbedx509-0_2.16.9-0.1 libmd0_1.0.4-1 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnetpbm10_2:10.0-15.4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenjp2-7_2.4.0-3 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libpdfbox-java_1:1.8.16-2 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpixman-1-0_0.40.0-1 libpng16-16_1.6.37-3 libpq5_14.0-1 libpsl5_0.21.0-1.2 libptexenc1_2021.20210626.59705-1 libpython3-all-dev_3.9.2-3 libpython3-dev_3.9.2-3 libpython3-stdlib_3.9.2-3 libpython3.9_3.9.7-4+rpi1 libpython3.9-dev_3.9.7-4+rpi1 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 libraqm0_0.7.0-4 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsm6_2:1.2.3-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-9+rpi1 libsub-override-perl_0.09-2 libsynctex2_2021.20210626.59705-1 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libteckit0_2.5.10+ds1-3 libtexlua53_2021.20210626.59705-1 libtexluajit2_2021.20210626.59705-1 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtiff5_4.3.0-2 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-9+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libwebp6_0.6.1-2.1 libwebpdemux2_0.6.1-2.1 libwebpmux3_0.6.1-2.1 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libxau6_1:1.0.9-1 libxaw7_2:1.0.13-1.1 libxcb-render0_1.14-3 libxcb-shm0_1.14-3 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxi6_2:1.8-1 libxml2_2.9.12+dfsg-5 libxmu6_2:1.1.2-2+b3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.2.0-1 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 mafft_7.487-1 mailcap_3.70 make_4.3-4.1 man-db_2.9.4-2 mariadb-common_1:10.5.12-1 mawk_1.3.4.20200120-2 media-types_4.0.0 mime-support_3.66 mount_2.37.2-1 muscle_1:3.8.1551-2 mysql-common_5.8+1.0.7 ncbi-blast+_2.11.0+ds-1 ncbi-data_6.1.20170106+dfsg1-9 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netpbm_2:10.0-15.4 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 phylip_1:3.697+dfsg-2 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 poppler-data_0.4.11-1 prank_0.0.170427+dfsg-3 preview-latex-style_12.2-1 probcons_1.12-14 python-matplotlib-data_3.3.4-2 python3_3.9.2-3 python3-all_3.9.2-3 python3-all-dev_3.9.2-3 python3-cycler_0.10.0-3 python3-dateutil_2.8.1-6 python3-decorator_4.4.2-2 python3-dev_3.9.2-3 python3-distutils_3.9.7-1 python3-isodate_0.6.0-2 python3-kiwisolver_1.3.2-1 python3-lib2to3_3.9.7-1 python3-linecache2_1.0.0-4 python3-matplotlib_3.3.4-2 python3-minimal_3.9.2-3 python3-mmtf_1.1.2-3 python3-msgpack_1.0.2-2 python3-mysqldb_1.4.4-2+b1 python3-networkx_2.5+ds-2 python3-numpy_1:1.19.5-1 python3-pil_8.3.2-1 python3-pkg-resources_58.2.0-1 python3-psycopg2_2.8.6-2 python3-pygments_2.7.1+dfsg-2.1 python3-pyparsing_2.4.7-1 python3-rdflib_5.0.0-1.1 python3-renderpm_3.5.59-2 python3-reportlab_3.5.59-2 python3-reportlab-accel_3.5.59-2 python3-scipy_1.6.0-2 python3-setuptools_58.2.0-1 python3-six_1.16.0-2 python3-traceback2_1.4.0-6 python3-unittest2_1.1.0-7 python3.9_3.9.7-4+rpi1 python3.9-dev_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 samtools_1.13-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 t-coffee_13.41.0.28bdc39+dfsg-4 t1utils_1.41-4 tar_1.34+dfsg-1 tex-common_6.17 texlive-base_2021.20210921-1 texlive-binaries_2021.20210626.59705-1 texlive-fonts-recommended_2021.20210921-1 texlive-latex-base_2021.20210921-1 texlive-latex-extra_2021.20210921-1 texlive-latex-recommended_2021.20210921-1 texlive-pictures_2021.20210921-1 ttf-bitstream-vera_1.10-8.1 tzdata_2021a-1 ucf_3.0043 util-linux_2.37.2-1 wise_2.4.1-23 wise-data_2.4.1-23 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

+------------------------------------------------------------------------------+
| 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: 1.79+dfsg-1
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: 4.6.0
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@
Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-numpy <!nocheck>, flex, python3-reportlab <!nocheck>, hevea <!nocheck>, 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>, muscle <!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-renderpm <!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:
 8eff51eb36ef780f81ae7d8679c95b89d0c113a2 9861184 python-biopython_1.79+dfsg.orig.tar.xz
 a27090125781265f01ee454e4bd72cfe41dc0e80 18272 python-biopython_1.79+dfsg-1.debian.tar.xz
Checksums-Sha256:
 cbb9fcc75832a13e4fee36df837395be8396a4843321bba5e7ddc03da8267583 9861184 python-biopython_1.79+dfsg.orig.tar.xz
 21196c04d10172bdae76544b21cf5367fa859d9d8a452f5d3ca0b704b32e52f5 18272 python-biopython_1.79+dfsg-1.debian.tar.xz
Files:
 437bb834cc474ff60ebd7dfb8d229d34 9861184 python-biopython_1.79+dfsg.orig.tar.xz
 82a488c31074bf326f8e78f66a4fc159 18272 python-biopython_1.79+dfsg-1.debian.tar.xz

-----BEGIN PGP SIGNATURE-----
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=8oph
-----END PGP SIGNATURE-----

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.DDQUpskl/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 22 19:22:40 2021 UTC
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-biopython_1.79+dfsg-1.dsc
dpkg-source: info: extracting python-biopython in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking python-biopython_1.79+dfsg.orig.tar.xz
dpkg-source: info: unpacking python-biopython_1.79+dfsg-1.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 mkdssp4.patch
dpkg-source: info: applying adjust-test_GraphicsBitmaps.patch
dpkg-source: info: applying spelling.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=359bbe4d259442eb9d8f94db1683c24a
JOURNAL_STREAM=8:21869
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
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-29ba56e0-c33c-4894-a9a2-7530756e1b17
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c18349
XDG_SESSION_TYPE=unspecified

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

Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package python-biopython
dpkg-buildpackage: info: source version 1.79+dfsg-1
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
	install -d /<<BUILDDIR>>/python-biopython-1.79\+dfsg/debian/.debhelper/generated/_source/home
	pybuild --clean -i python{version} -p 3.9
I: pybuild base:232: python3.9 setup.py clean 
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
  warnings.warn(
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.9' 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
( 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
	install -d /<<BUILDDIR>>/python-biopython-1.79\+dfsg/debian/.debhelper/generated/_source/home
	pybuild --configure -i python{version} -p 3.9
I: pybuild base:232: python3.9 setup.py config 
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
  warnings.warn(
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
	pybuild --build -i python{version} -p 3.9
I: pybuild base:232: /usr/bin/python3 setup.py build 
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
  warnings.warn(
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/File.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/LogisticRegression.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/MarkovModel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/MaxEntropy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/NaiveBayes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/Seq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/SeqFeature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/SeqRecord.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/bgzf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/kNN.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/pairwise2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Affy
copying Bio/Affy/CelFile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Affy
copying Bio/Affy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Affy
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align
copying Bio/Align/AlignInfo.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align
copying Bio/Align/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices
copying Bio/Align/substitution_matrices/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/MsfIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Alphabet
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Application
copying Bio/Application/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Application
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast
copying Bio/Blast/Applications.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast
copying Bio/Blast/NCBIXML.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast
copying Bio/Blast/Record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast
copying Bio/Blast/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/CAPS
copying Bio/CAPS/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/CAPS
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster
copying Bio/Cluster/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign
copying Bio/codonalign/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign
copying Bio/codonalign/chisq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign
copying Bio/codonalign/codonseq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Compass
copying Bio/Compass/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Compass
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data
copying Bio/Data/CodonTable.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data
copying Bio/Data/IUPACData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data
copying Bio/Data/SCOPData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data
copying Bio/Data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss
copying Bio/Emboss/Applications.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss
copying Bio/Emboss/Primer3.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss
copying Bio/Emboss/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez
copying Bio/Entrez/Parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez
copying Bio/Entrez/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank
copying Bio/GenBank/Record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank
copying Bio/GenBank/Scanner.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank
copying Bio/GenBank/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank
copying Bio/GenBank/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Geo
copying Bio/Geo/Record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Geo
copying Bio/Geo/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Geo
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics
copying Bio/Graphics/Comparative.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics
copying Bio/Graphics/Distribution.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics
copying Bio/Graphics/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM
copying Bio/HMM/MarkovModel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM
copying Bio/HMM/Trainer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM
copying Bio/HMM/Utilities.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM
copying Bio/HMM/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG
copying Bio/KEGG/REST.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG
copying Bio/KEGG/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Compound
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Enzyme
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Gene
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Map
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/mmtfio.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Medline
copying Bio/Medline/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Medline
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/alignace.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/clusterbuster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/mast.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/matrix.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/meme.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/minimal.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/pfm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/thresholds.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/transfac.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/motifs/xms.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/applications
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus
copying Bio/Nexus/Nexus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus
copying Bio/Nexus/Nodes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus
copying Bio/Nexus/StandardData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus
copying Bio/Nexus/Trees.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus
copying Bio/Nexus/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR
copying Bio/NMR/NOEtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR
copying Bio/NMR/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR
copying Bio/NMR/xpktools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway
copying Bio/Pathway/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep
copying Bio/PDB/AbstractPropertyMap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Atom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Chain.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Dice.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Entity.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/HSExposure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Model.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/NACCESS.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/PDBIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/PDBList.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/PDBParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/PICIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/PSEA.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Polypeptide.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Residue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/SASA.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/SCADIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Selection.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Structure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/Superimposer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/ic_data.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/ic_rebuild.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/internal_coords.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/mmcifio.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/vectors.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/PDB/DSSP.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype
copying Bio/phenotype/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen
copying Bio/PopGen/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction
copying Bio/Restriction/Restriction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction
copying Bio/Restriction/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP
copying Bio/SCOP/Cla.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP
copying Bio/SCOP/Des.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP
copying Bio/SCOP/Dom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP
copying Bio/SCOP/Hie.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP
copying Bio/SCOP/Raf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP
copying Bio/SCOP/Residues.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP
copying Bio/SCOP/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO
copying Bio/SearchIO/_index.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/GckIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/SnapGeneIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/TwoBitIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/XdnaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/SeqIO/_index.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat
copying Bio/SubsMat/FreqTable.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat
copying Bio/SubsMat/MatrixInfo.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat
copying Bio/SubsMat/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SVDSuperimposer
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SwissProt
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/TogoWS
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/CDAO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/Consensus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/NeXML.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/Newick.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/_io.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
copying Bio/Phylo/_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniGene
copying Bio/UniGene/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniGene
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniProt
copying Bio/UniProt/GOA.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniProt
copying Bio/UniProt/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniProt
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise
copying Bio/Wise/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise
copying Bio/Wise/dnal.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise
copying Bio/Wise/psw.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL
copying BioSQL/BioSeq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL
copying BioSQL/BioSeqDatabase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL
copying BioSQL/DBUtils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL
copying BioSQL/Loader.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL
copying BioSQL/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/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'
copying Bio/cpairwise2module.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio
copying Bio/Align/_aligners.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER22 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER6 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER74 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/FENG -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GENETIC -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/HOXD70 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JOHNSON -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JONES -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/LEVIN -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MDM78 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM250 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM30 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM70 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RAO -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RISLER -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/STR -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/TRANS -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data
copying Bio/Cluster/cluster.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster
copying Bio/Cluster/cluster.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivearticle.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/articlemeta.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/backmatter.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/chars.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/common.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-classes.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-mixes.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/display.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSearch_020511.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSpell.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSummary_041029.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/egquery.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/einfo.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/elink_020122.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esearch.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/format.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/htmltable.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsa.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsb.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsc.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsn.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamso.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsr.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isobox.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr1.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr2.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isodia.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk1.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk2.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk3.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk4.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat1.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat2.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomfrk.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomopf.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomscr.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isonum.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isopub.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isotech.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/journalmeta.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/link.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/list.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/math.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlalias.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlextra.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/modules.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pmc-1.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/taxon.dtd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs
copying Bio/Nexus/cnexus.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus
copying Bio/PDB/kdtrees.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB
copying Bio/SeqIO/_twoBitIO.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer
running build_ext
building 'Bio.Align._aligners' extension
creating build
creating build/temp.linux-armhf-3.9
creating build/temp.linux-armhf-3.9/Bio
creating build/temp.linux-armhf-3.9/Bio/Align
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/Align/_aligners.c -o build/temp.linux-armhf-3.9/Bio/Align/_aligners.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/Bio/Align/_aligners.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/_aligners.cpython-39-arm-linux-gnueabihf.so
building 'Bio.cpairwise2' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/cpairwise2module.c -o build/temp.linux-armhf-3.9/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/python3.9/Python.h:154,
                 from Bio/cpairwise2module.c:16:
/usr/include/python3.9/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/Bio/cpairwise2module.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/cpairwise2.cpython-39-arm-linux-gnueabihf.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-armhf-3.9/Bio/Nexus
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/Nexus/cnexus.c -o build/temp.linux-armhf-3.9/Bio/Nexus/cnexus.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/Bio/Nexus/cnexus.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/cnexus.cpython-39-arm-linux-gnueabihf.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-armhf-3.9/Bio/PDB
creating build/temp.linux-armhf-3.9/Bio/PDB/QCPSuperimposer
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armhf-3.9/Bio/PDB/QCPSuperimposer/qcprotmodule.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-arm-linux-gnueabihf.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-armhf-3.9/Bio/motifs
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/motifs/_pwm.c -o build/temp.linux-armhf-3.9/Bio/motifs/_pwm.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/Bio/motifs/_pwm.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/_pwm.cpython-39-arm-linux-gnueabihf.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-armhf-3.9/Bio/Cluster
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/Cluster/cluster.c -o build/temp.linux-armhf-3.9/Bio/Cluster/cluster.o
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armhf-3.9/Bio/Cluster/clustermodule.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/Bio/Cluster/cluster.o build/temp.linux-armhf-3.9/Bio/Cluster/clustermodule.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster/_cluster.cpython-39-arm-linux-gnueabihf.so
building 'Bio.PDB.kdtrees' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/PDB/kdtrees.c -o build/temp.linux-armhf-3.9/Bio/PDB/kdtrees.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/Bio/PDB/kdtrees.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/kdtrees.cpython-39-arm-linux-gnueabihf.so
building 'Bio.SeqIO._twoBitIO' extension
creating build/temp.linux-armhf-3.9/Bio/SeqIO
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-armhf-3.9/Bio/SeqIO/_twoBitIO.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/Bio/SeqIO/_twoBitIO.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/_twoBitIO.cpython-39-arm-linux-gnueabihf.so
cd Doc && make
make[2]: Entering directory '/<<PKGBUILDDIR>>/Doc'
sed "s/\@VERSION\@/1.79/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:186: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_introduction.tex:192: 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:85: Warning: Undefined label: 'sec:mutable-seq'
./Tutorial/chapter_seq_objects.tex:154: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:268: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_seq_objects.tex:343: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:457: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seq_objects.tex:463: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:586: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:744: Warning: Undefined label: 'chapter:seqio'
./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:21: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:34: Warning: Undefined label: 'sec:FASTQ-filtering-example'
./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seq_annot.tex:133: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:212: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:276: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:279: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:525: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:627: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:678: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_seq_annot.tex:820: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_annot.tex:832: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer'
./Tutorial/chapter_seq_annot.tex:833: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor'
./Tutorial/chapter_seq_annot.tex:846: 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:13: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seqio.tex:15: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_seqio.tex:23: Warning: Undefined label: 'sec:SeqIO_Online'
./Tutorial/chapter_seqio.tex:23: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:44: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_seqio.tex:69: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab'
./Tutorial/chapter_seqio.tex:151: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:310: Warning: Undefined label: 'sec:writing-sequence-files'
./Tutorial/chapter_seqio.tex:330: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:333: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:401: Warning: Undefined label: 'sec:SeqIO-index-bgzf'
./Tutorial/chapter_seqio.tex:404: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:417: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_seqio.tex:507: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_seqio.tex:507: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:512: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_seqio.tex:568: Warning: Undefined label: 'sec:seqio_todict'
./Tutorial/chapter_seqio.tex:574: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-index-db'
./Tutorial/chapter_seqio.tex:581: Warning: Undefined label: 'sec:SeqIO-indexing-discussion'
./Tutorial/chapter_seqio.tex:584: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:591: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:665: Warning: Undefined label: 'sec:fasta-parsing'
./Tutorial/chapter_seqio.tex:786: Warning: Undefined label: 'sec:fastq-indexing'
./Tutorial/chapter_seqio.tex:807: Warning: Undefined label: 'sec:seqio-todict-functionkey'
./Tutorial/chapter_seqio.tex:869: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_seqio.tex:951: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1192: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1236: Warning: Undefined label: 'sec:SeqIO-fastq-conversion'
./Tutorial/chapter_seqio.tex:1236: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion'
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined label: 'sec:seq-reverse-complement'
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_seqio.tex:1303: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seqio.tex:1404: 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:915: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_align.tex:919: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_align.tex:949: Warning: Undefined label: 'sec:emboss-needle-water'
./Tutorial/chapter_align.tex:957: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:1095: Warning: Undefined label: 'chapter:phylo'
./Tutorial/chapter_align.tex:1316: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:1688: Warning: Undefined citation: 'durbin1998'
./Tutorial/chapter_align.tex:1701: Warning: Undefined label: 'sec:pairwise-aligner'
./Tutorial/chapter_align.tex:1774: Warning: Undefined citation: 'waterman1987'
./Tutorial/chapter_align.tex:1804: Warning: Undefined label: 'sec:pairwise-substitution-scores'
./Tutorial/chapter_align.tex:1804: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1804: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1805: Warning: Undefined label: 'sec:pairwise-basic'
./Tutorial/chapter_align.tex:1808: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1809: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1835: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1835: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1864: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1968: Warning: Undefined label: 'table:align-meta-attributes'
./Tutorial/chapter_align.tex:2058: Warning: Undefined label: 'sec:pairwise-examples'
./Tutorial/chapter_align.tex:2486: Warning: Undefined citation: 'kent2002'
./Tutorial/chapter_align.tex:2555: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2763: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:2763: Warning: Undefined label: 'sec:substitution_matrices'
./Tutorial/chapter_align.tex:2969: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:3319: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:3391: Warning: Undefined citation: 'henikoff1992'
./Tutorial/chapter_align.tex:3391: Warning: Undefined citation: 'dayhoff1978'
./Tutorial/chapter_align.tex:3415: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio'
./Tutorial/chapter_blast.tex:58: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:119: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:124: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:146: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:155: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:164: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:192: Warning: Undefined label: 'sec:alignment-tools'
./Tutorial/chapter_blast.tex:236: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:286: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:288: Warning: Undefined label: 'sec:running-local-blast'
./Tutorial/chapter_blast.tex:303: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_blast.tex:339: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:339: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_blast.tex:449: Warning: Undefined label: 'fig:blastrecord'
./Tutorial/chapter_blast.tex:465: Warning: Undefined label: 'fig:psiblastrecord'
./Tutorial/chapter_searchio.tex:734: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_searchio.tex:1082: 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:234: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:297: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:323: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:323: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:417: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:479: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:481: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:562: Warning: Undefined label: 'sec:elink-citations'
./Tutorial/chapter_entrez.tex:568: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:777: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:777: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:897: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1058: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1061: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1065: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1108: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1154: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1206: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1241: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1248: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:1249: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:1325: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_entrez.tex:1326: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1386: Warning: Undefined label: 'sec:entrez-search-fetch-genbank'
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:1496: Warning: Undefined label: 'sec:entrez-and-medline'
./Tutorial/chapter_entrez.tex:1501: Warning: Undefined label: 'sec:elink'
./Tutorial/chapter_entrez.tex:1525: 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:341: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:343: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_pdb.tex:85: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:276: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:285: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:422: Warning: Undefined label: 'sec:hetero_problems'
./Tutorial/chapter_pdb.tex:467: Warning: Undefined label: 'sec:point_mutations'
./Tutorial/chapter_pdb.tex:484: Warning: Undefined label: 'sec:disordered_atoms'
./Tutorial/chapter_pdb.tex:593: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:607: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:611: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:647: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:658: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:684: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:970: Warning: Undefined label: 'table:ic-attribs'
./Tutorial/chapter_pdb.tex:1015: Warning: Undefined citation: 'golub1989'
./Tutorial/chapter_pdb.tex:1043: Warning: Undefined citation: 'hamelryck2005'
./Tutorial/chapter_pdb.tex:1078: Warning: Undefined label: 'table:DSSP-codes'
./Tutorial/chapter_pdb.tex:1118: Warning: Undefined label: 'sec:residue_depth'
./Tutorial/chapter_pdb.tex:1121: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1169: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_pdb.tex:1183: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1380: Warning: Undefined citation: 'hamelryck2003b'
./Tutorial/chapter_pdb.tex:1381: 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:192: Warning: Undefined label: 'fig:phylo-color-draw'
./Tutorial/chapter_phylo.tex:715: Warning: Undefined label: 'sec:alignment-tools'
./Tutorial/chapter_phylo.tex:786: Warning: Undefined label: 'sec:PhyloXML'
./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links'
./Tutorial/chapter_motifs.tex:164: Warning: Undefined citation: 'cornish1985'
./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cavener1987'
./Tutorial/chapter_motifs.tex:541: Warning: Undefined citation: 'bailey1994'
./Tutorial/chapter_motifs.tex:687: Warning: Undefined citation: 'matys2003'
./Tutorial/chapter_motifs.tex:771: 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:277: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:345: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:555: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:599: Warning: Undefined citation: 'kohonen1997'
./Tutorial/chapter_cluster.tex:599: Warning: Undefined citation: 'tamayo1999'
./Tutorial/chapter_cluster.tex:646: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:659: Warning: Undefined citation: 'yeung2001'
./Tutorial/chapter_cluster.tex:667: Warning: Undefined citation: 'golub1971'
./Tutorial/chapter_cluster.tex:800: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:803: Warning: Undefined label: 'sec:distancematrix'
./Tutorial/chapter_cluster.tex:821: Warning: Undefined label: 'sec:clustercentroids'
./Tutorial/chapter_cluster.tex:844: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:869: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:898: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:920: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:952: 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:212: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:212: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:274: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:274: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:276: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:276: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:286: Warning: Undefined label: 'sec:LogisticRegression'
./Tutorial/chapter_learning.tex:290: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:298: 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:229: Warning: Optional argument to \item in itemize environment
./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_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:199: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:204: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_cookbook.tex:336: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_cookbook.tex:441: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:455: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:478: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_cookbook.tex:641: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_cookbook.tex:800: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:822: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:824: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_cookbook.tex:838: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:1021: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_cookbook.tex:1038: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:1413: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1416: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1431: Warning: Undefined label: 'sec:consensus'
./Tutorial/chapter_cookbook.tex:1432: Warning: Undefined label: 'sec:pssm'
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined label: 'sec:getting_info_content'
./Tutorial/chapter_cookbook.tex:1434: Warning: Undefined label: 'sec:sub_matrix'
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1560: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1612: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1635: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_cookbook.tex:1741: 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_advanced.tex:36: Warning: Undefined label: 'sec:substitution_matrices'
./Tutorial/chapter_advanced.tex:162: Warning: Undefined label: 'sec:freq_table'
./Tutorial/chapter_advanced.tex:222: 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:85: Warning: Undefined label: 'chapter:testing'
./Tutorial/chapter_contributing.tex:101: 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_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:279: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:330: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:404: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:584: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:957: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2555: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2969: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1058: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1061: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:341: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:593: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:607: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:647: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:684: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1121: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1183: 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:229: Warning: Optional argument to \item in itemize environment
./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_cookbook.tex:1416: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1612: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode
./Tutorial/chapter_advanced.tex:222: 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:362: 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:153: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:153: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:157: 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:163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:163: 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:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:179: 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:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: 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:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:220: 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:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: 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:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode
./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:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:286: Warning: Command not found: \downarrow
./Tutorial/chapter_seq_objects.tex:295: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:295: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:458: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:458: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:689: 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:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:720: 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:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:773: 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:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:100: 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: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:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:121: Warning: '_' occurring outside math mode
./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 block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:140: Warning: line too long
./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:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:145: 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:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:219: Warning: line too long
./Tutorial/chapter_seq_annot.tex:228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:279: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:294: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:294: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:299: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:299: 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:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:321: 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:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:372: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:372: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:378: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:378: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:381: 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:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: line too long
./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:554: 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:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:574: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:574: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:595: 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: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:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:674: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:674: 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:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:695: Warning: line too long
./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:710: Warning: line too long
./Tutorial/chapter_seq_annot.tex:731: Warning: line too long
./Tutorial/chapter_seq_annot.tex:731: Warning: line too long
./Tutorial/chapter_seq_annot.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:742: Warning: line too long
./Tutorial/chapter_seq_annot.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:752: Warning: line too long
./Tutorial/chapter_seq_annot.tex:773: Warning: line too long
./Tutorial/chapter_seq_annot.tex:773: Warning: line too long
./Tutorial/chapter_seq_annot.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:907: Warning: line too long
./Tutorial/chapter_seq_annot.tex:924: Warning: line too long
./Tutorial/chapter_seq_annot.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:965: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:965: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:966: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:966: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:983: 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:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:44: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:44: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:94: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:94: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:94: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:94: 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:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:151: Warning: '_' occurring outside math mode
./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:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:199: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:249: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:294: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:294: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:295: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:295: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:312: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:312: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:330: Warning: '_' occurring outside math mode
./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:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:404: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:514: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:514: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:553: Warning: line too long
./Tutorial/chapter_seqio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:563: 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:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:575: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:575: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:584: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:604: 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:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:745: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:745: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:750: 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:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:822: 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:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:853: Warning: line too long
./Tutorial/chapter_seqio.tex:854: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:854: 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:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:937: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:937: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:950: 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:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:981: 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:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1037: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1037: 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:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1076: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1076: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1085: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1085: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1128: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1128: 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:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1160: 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:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1201: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:1221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1239: 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:1249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1341: 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:1347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1348: 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:1352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1352: 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:1359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1386: 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:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:862: 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:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:935: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:935: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:957: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1018: 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:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1026: 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:1052: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1052: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1071: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1071: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1494: 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:1501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1517: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1517: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1549: Warning: line too long
./Tutorial/chapter_align.tex:1551: Warning: line too long
./Tutorial/chapter_align.tex:1569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1592: 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 block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1629: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1629: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1653: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1653: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1693: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1693: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1719: 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:1750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1752: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1752: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1752: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1752: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1753: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1753: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1754: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1754: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1779: 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:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1926: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1926: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1926: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1926: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1968: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1968: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: 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:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: 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: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:1989: 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:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1992: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1992: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1997: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1997: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: 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:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2014: Warning: overfull line in array : array too wide
./Tutorial/chapter_align.tex:2014: Warning: line too long
./Tutorial/chapter_align.tex:2014: Warning: line too long
./Tutorial/chapter_align.tex:2014: Warning: line too long
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2096: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2096: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2296: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2296: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2409: Warning: line too long
./Tutorial/chapter_align.tex:2425: Warning: line too long
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2490: Warning: line too long
./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:2495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2555: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2578: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2578: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2578: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2578: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2695: Warning: line too long
./Tutorial/chapter_align.tex:2696: Warning: line too long
./Tutorial/chapter_align.tex:2697: Warning: line too long
./Tutorial/chapter_align.tex:2727: Warning: line too long
./Tutorial/chapter_align.tex:2728: Warning: line too long
./Tutorial/chapter_align.tex:2729: Warning: line too long
./Tutorial/chapter_align.tex:2736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2969: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: 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:2988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3012: 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:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3086: 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:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3300: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3300: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3387: 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: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 block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3406: 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: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:50: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:50: Warning: Undefined block in text mode: 'CODE' []
./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:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:57: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:57: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:59: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:59: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:95: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:95: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:118: 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 block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:258: 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:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: 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:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:437: Warning: line too long
./Tutorial/chapter_blast.tex:439: Warning: line too long
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:453: Warning: Image in text
./Tutorial/chapter_blast.tex:469: Warning: Image in text
./Tutorial/chapter_blast.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:504: 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:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:262: 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:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:314: 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:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:351: 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:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:358: 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:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:387: 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:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:390: 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:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:403: 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:404: 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: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: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: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:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:412: 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:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:438: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:438: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:438: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:438: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:442: 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: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:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:502: 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:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:553: 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:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:559: 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:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:585: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:585: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:585: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:585: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: 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:616: 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:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: 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:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:625: 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:628: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:628: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:629: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:629: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:695: 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:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:728: Warning: line too long
./Tutorial/chapter_searchio.tex:730: Warning: line too long
./Tutorial/chapter_searchio.tex:733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:736: Warning: Undefined block in text mode: 'CODE' []
./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 block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:739: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:739: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:739: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:751: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:751: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:844: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:844: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: 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:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:880: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:880: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:880: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:880: 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:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:905: 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:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:912: 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:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:961: Warning: line too long
./Tutorial/chapter_searchio.tex:968: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:968: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:998: 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:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1006: 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:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1019: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1019: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1019: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1019: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1020: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1020: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1020: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1020: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1022: 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:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1026: 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:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1052: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1052: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1076: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1076: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1077: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1077: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1081: 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:1086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1125: 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:1133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1170: 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:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:300: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:300: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: 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:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:415: 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:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:479: 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 block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:863: 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:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:943: Warning: line too long
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1025: 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:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1040: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1040: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1058: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1061: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1078: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1078: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1395: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1395: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1496: 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:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: 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:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:314: 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:316: 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:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:341: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:442: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:442: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:491: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:491: 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:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:87: 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:115: 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: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:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: 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:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:126: 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:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:289: Warning: Image in text
./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:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:392: 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:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:593: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:607: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:647: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:684: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:769: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:769: 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:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:992: Warning: overfull line in array : array too wide
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:1121: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1183: 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:104: Warning: Image in text
./Tutorial/chapter_phylo.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:186: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:186: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:199: Warning: Image in text
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:256: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:256: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:268: 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:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:293: 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:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:346: Warning: line too long
./Tutorial/chapter_phylo.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:360: Warning: Image in text
./Tutorial/chapter_phylo.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:482: 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:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:508: 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:571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:576: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:576: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:607: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:607: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:628: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:628: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:700: 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_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:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:209: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:209: 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:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:256: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:256: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:549: Warning: line too long
./Tutorial/chapter_motifs.tex:551: Warning: line too long
./Tutorial/chapter_motifs.tex:557: Warning: line too long
./Tutorial/chapter_motifs.tex:559: Warning: line too long
./Tutorial/chapter_motifs.tex:568: Warning: line too long
./Tutorial/chapter_motifs.tex:572: Warning: line too long
./Tutorial/chapter_motifs.tex:574: Warning: line too long
./Tutorial/chapter_motifs.tex:583: Warning: line too long
./Tutorial/chapter_motifs.tex:585: Warning: line too long
./Tutorial/chapter_motifs.tex:586: Warning: line too long
./Tutorial/chapter_motifs.tex:588: Warning: line too long
./Tutorial/chapter_motifs.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:602: 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:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:619: 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:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:711: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:711: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:746: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:746: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:756: 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:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:778: 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:802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:809: 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:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:907: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:907: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:959: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:959: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1043: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1043: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1064: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1064: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1092: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1092: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1092: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1092: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1101: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1101: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: 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:1166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1166: 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:1188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1312: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1312: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1512: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1512: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1529: 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:1564: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: 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:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:234: 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: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: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: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: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:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:259: 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: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: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:270: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:270: 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:276: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:276: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:276: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:276: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: 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: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:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:329: 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: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: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: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: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:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:340: 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:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:343: 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:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:346: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:346: 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: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: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: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:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:383: 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: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: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:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:418: 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:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:512: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:512: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:514: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:514: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:518: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:518: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:520: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:520: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:538: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:538: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:540: 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: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: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: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:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:549: 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:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:582: 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:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:586: 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:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:606: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:610: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:615: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:624: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:624: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:633: 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: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: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: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:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:641: 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:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:653: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:653: 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:654: 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:654: 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:654: 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:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:674: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:674: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:676: 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:682: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:682: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:710: Warning: line too long
./Tutorial/chapter_cluster.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:712: Warning: Undefined block in text mode: 'CODE' []
./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:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:747: Warning: overfull line in array : array too wide
./Tutorial/chapter_cluster.tex:747: Warning: line too long
./Tutorial/chapter_cluster.tex:747: Warning: line too long
./Tutorial/chapter_cluster.tex:753: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:753: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: 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:765: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:765: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:766: 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:769: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:769: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:769: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:769: 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:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:772: 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:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:778: 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:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:781: 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:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: 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:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:814: 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: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: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: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:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:830: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:830: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:830: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:830: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:831: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:831: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:831: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:831: 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:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:838: 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:843: 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: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 block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: 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:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: 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:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:864: 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:868: 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: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:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:884: 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:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: 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: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:893: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:893: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:894: 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:897: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:897: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:897: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:897: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:911: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:911: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:911: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:911: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: 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: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:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:916: 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: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:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:923: 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:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:940: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:940: 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:942: 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: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:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:950: 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:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: 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:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: 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:302: 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:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:408: Warning: Application of '\"' on 'i' failed
./Tutorial/chapter_learning.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:418: 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:229: Warning: Optional argument to \item in itemize environment
./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_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:199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:203: 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 block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:250: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:250: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:324: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:324: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:332: 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:335: 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:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:355: 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:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:395: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:395: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:450: Warning: line too long
./Tutorial/chapter_cookbook.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:452: Warning: Undefined block in text mode: 'CODE' []
./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:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:458: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:458: 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:478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:559: Warning: line too long
./Tutorial/chapter_cookbook.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:591: Warning: Undefined block in text mode: 'CODE' []
./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:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:653: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:684: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:693: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:693: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:713: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:713: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:713: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:713: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:763: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:763: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:763: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:763: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:765: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:765: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:803: Warning: line too long
./Tutorial/chapter_cookbook.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:825: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:825: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:838: 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:1028: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1028: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1050: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1091: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1091: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1124: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1158: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1158: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1206: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1260: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1260: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1336: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1336: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1336: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1358: Warning: line too long
./Tutorial/chapter_cookbook.tex:1359: Warning: line too long
./Tutorial/chapter_cookbook.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1407: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1416: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1579: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1579: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1612: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1736: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1741: 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_advanced.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:50: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:50: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:64: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:64: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:222: Warning: '_' occurring outside math mode
./Tutorial/chapter_advanced.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:254: 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:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:80: 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:127: Warning: line too long
./Tutorial.tex:138: Warning: Application of '\'' on 'e' failed
./Tutorial.tex:138: Warning: Application of '\'' on 'o' failed
./Tutorial.tex:142: Warning: Application of '\"' on 'u' failed
./Tutorial.tex:216: Warning: Application of '\"' on 'o' failed
./Tutorial.tex:216: 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:547: 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:153: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:153: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:157: 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:163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:163: 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:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:179: 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:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:186: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_introduction.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:192: Warning: Undefined label: 'sec:appendix-handles'
./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:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:220: 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:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:230: 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:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:233: 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:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined label: 'sec:mutable-seq'
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:154: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:268: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_seq_objects.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:286: Warning: Command not found: \downarrow
./Tutorial/chapter_seq_objects.tex:295: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:295: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:343: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:457: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seq_objects.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:458: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:458: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:463: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:586: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:683: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:689: 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:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:720: 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:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:744: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:773: 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:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:34: Warning: Undefined label: 'sec:FASTQ-filtering-example'
./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:100: 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: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:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:121: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined label: 'chapter:quick_start'
./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 block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:133: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:140: Warning: line too long
./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:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:145: 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:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:212: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:219: Warning: line too long
./Tutorial/chapter_seq_annot.tex:228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:228: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:276: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:279: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:285: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:294: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:294: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:299: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:299: 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:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:321: 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:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:372: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:372: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:378: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:378: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:381: 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:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:525: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:531: Warning: line too long
./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:554: 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:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:574: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:574: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:595: 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: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:627: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_seq_annot.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:635: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:674: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:674: 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 label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:678: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:695: Warning: line too long
./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:710: Warning: line too long
./Tutorial/chapter_seq_annot.tex:731: Warning: line too long
./Tutorial/chapter_seq_annot.tex:731: Warning: line too long
./Tutorial/chapter_seq_annot.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:742: Warning: line too long
./Tutorial/chapter_seq_annot.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:752: Warning: line too long
./Tutorial/chapter_seq_annot.tex:773: Warning: line too long
./Tutorial/chapter_seq_annot.tex:773: Warning: line too long
./Tutorial/chapter_seq_annot.tex:820: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_annot.tex:832: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer'
./Tutorial/chapter_seq_annot.tex:833: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor'
./Tutorial/chapter_seq_annot.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:846: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:907: Warning: line too long
./Tutorial/chapter_seq_annot.tex:924: Warning: line too long
./Tutorial/chapter_seq_annot.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:965: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:965: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:966: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:966: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:983: 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:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:13: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seqio.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:15: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_seqio.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:23: Warning: Undefined label: 'sec:SeqIO_Online'
./Tutorial/chapter_seqio.tex:23: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:44: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_seqio.tex:44: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:44: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:69: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab'
./Tutorial/chapter_seqio.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:94: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:94: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:94: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:94: 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:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:151: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:151: Warning: '_' occurring outside math mode
./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:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:199: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:249: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:294: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:294: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:295: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:295: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:310: Warning: Undefined label: 'sec:writing-sequence-files'
./Tutorial/chapter_seqio.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:312: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:312: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:330: Warning: '_' occurring outside math mode
./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 label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:401: Warning: Undefined label: 'sec:SeqIO-index-bgzf'
./Tutorial/chapter_seqio.tex:404: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:416: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:417: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_seqio.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:507: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_seqio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:507: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:510: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:512: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_seqio.tex:514: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:514: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:553: Warning: line too long
./Tutorial/chapter_seqio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:563: 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:568: Warning: Undefined label: 'sec:seqio_todict'
./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:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:574: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:575: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:575: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-index-db'
./Tutorial/chapter_seqio.tex:581: Warning: Undefined label: 'sec:SeqIO-indexing-discussion'
./Tutorial/chapter_seqio.tex:584: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:604: 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:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:665: Warning: Undefined label: 'sec:fasta-parsing'
./Tutorial/chapter_seqio.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:723: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:745: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:745: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:750: 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:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:786: Warning: Undefined label: 'sec:fastq-indexing'
./Tutorial/chapter_seqio.tex:807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:807: Warning: Undefined label: 'sec:seqio-todict-functionkey'
./Tutorial/chapter_seqio.tex:822: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:822: 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:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:853: Warning: line too long
./Tutorial/chapter_seqio.tex:854: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:854: 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:869: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_seqio.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:937: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:937: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:951: Warning: Undefined label: 'sec:seqio-index-getraw'
./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:981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:981: 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:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1037: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1037: 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:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1076: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1076: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1085: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1085: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1128: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1128: 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:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1160: 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:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1192: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1201: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:1221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1236: Warning: Undefined label: 'sec:SeqIO-fastq-conversion'
./Tutorial/chapter_seqio.tex:1236: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion'
./Tutorial/chapter_seqio.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1239: 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:1249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1251: Warning: Undefined label: 'sec:seq-reverse-complement'
./Tutorial/chapter_seqio.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1261: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_seqio.tex:1303: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seqio.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1323: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seqio.tex:1325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1341: 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:1347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1348: 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:1352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1352: 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:1359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1404: 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:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:862: 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:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:915: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_align.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:919: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_align.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:935: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:935: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:949: Warning: Undefined label: 'sec:emboss-needle-water'
./Tutorial/chapter_align.tex:957: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1018: 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:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1026: 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:1052: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1052: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1071: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1071: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1095: Warning: Undefined label: 'chapter:phylo'
./Tutorial/chapter_align.tex:1100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1316: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:1376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1494: 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:1501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1517: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1517: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1549: Warning: line too long
./Tutorial/chapter_align.tex:1551: Warning: line too long
./Tutorial/chapter_align.tex:1569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1592: 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 block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1629: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1629: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1653: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1653: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1688: Warning: Undefined citation: 'durbin1998'
./Tutorial/chapter_align.tex:1693: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1693: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1701: Warning: Undefined label: 'sec:pairwise-aligner'
./Tutorial/chapter_align.tex:1719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1719: 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:1750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1752: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1752: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1752: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1752: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1753: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1753: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1754: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1754: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1774: Warning: Undefined citation: 'waterman1987'
./Tutorial/chapter_align.tex:1779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined label: 'sec:pairwise-substitution-scores'
./Tutorial/chapter_align.tex:1804: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1804: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./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 label: 'sec:pairwise-basic'
./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:1808: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1809: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./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:1819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1906: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1926: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1926: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1926: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1926: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1968: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1968: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1968: Warning: Undefined label: 'table:align-meta-attributes'
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1977: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1980: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1981: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1983: 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:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1987: 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: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:1989: 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:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1990: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1992: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1992: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1997: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1997: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1998: 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:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2001: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2014: Warning: overfull line in array : array too wide
./Tutorial/chapter_align.tex:2014: Warning: line too long
./Tutorial/chapter_align.tex:2014: Warning: line too long
./Tutorial/chapter_align.tex:2014: Warning: line too long
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2058: Warning: Undefined label: 'sec:pairwise-examples'
./Tutorial/chapter_align.tex:2060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2060: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2096: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2096: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2296: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2296: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2409: Warning: line too long
./Tutorial/chapter_align.tex:2425: Warning: line too long
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2486: Warning: Undefined citation: 'kent2002'
./Tutorial/chapter_align.tex:2490: Warning: line too long
./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:2495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2495: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2555: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2578: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2578: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2578: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2578: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2671: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2695: Warning: line too long
./Tutorial/chapter_align.tex:2696: Warning: line too long
./Tutorial/chapter_align.tex:2697: Warning: line too long
./Tutorial/chapter_align.tex:2727: Warning: line too long
./Tutorial/chapter_align.tex:2728: Warning: line too long
./Tutorial/chapter_align.tex:2729: Warning: line too long
./Tutorial/chapter_align.tex:2736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2763: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:2763: Warning: Undefined label: 'sec:substitution_matrices'
./Tutorial/chapter_align.tex:2796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2969: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2971: 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:2988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3012: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3012: 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:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3086: 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:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3269: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3300: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3300: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3319: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:3319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined citation: 'henikoff1992'
./Tutorial/chapter_align.tex:3391: Warning: Undefined citation: 'dayhoff1978'
./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 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:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3415: Warning: Undefined citation: 'schneider2005'
./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: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:50: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:50: Warning: Undefined block in text mode: 'CODE' []
./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:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:56: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:57: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:57: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:58: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:59: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:59: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:95: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:95: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:119: Warning: Undefined label: 'chapter:seqio'
./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:124: Warning: Undefined label: 'sec:parsing-blast'
./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 block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:146: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:155: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:164: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:192: Warning: Undefined label: 'sec:alignment-tools'
./Tutorial/chapter_blast.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:258: 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:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:286: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:288: Warning: Undefined label: 'sec:running-local-blast'
./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_blast.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:339: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_blast.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: 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:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:437: Warning: line too long
./Tutorial/chapter_blast.tex:439: Warning: line too long
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:449: Warning: Undefined label: 'fig:blastrecord'
./Tutorial/chapter_blast.tex:453: Warning: Image in text
./Tutorial/chapter_blast.tex:465: Warning: Undefined label: 'fig:psiblastrecord'
./Tutorial/chapter_blast.tex:469: Warning: Image in text
./Tutorial/chapter_blast.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:504: 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:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:262: 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:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:314: 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:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:351: 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:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:358: 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:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:387: 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:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:390: 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:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:403: 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:404: 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: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: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: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:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:412: 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:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:438: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:438: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:438: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:438: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:442: 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: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:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:502: 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:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:553: 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:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:559: 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:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:585: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:585: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:585: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:585: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:614: 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:616: 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:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:617: 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:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:625: 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:628: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:628: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:629: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:629: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:695: 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:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:728: Warning: line too long
./Tutorial/chapter_searchio.tex:730: Warning: line too long
./Tutorial/chapter_searchio.tex:733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:734: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_searchio.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:735: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:736: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:736: Warning: Undefined block in text mode: 'CODE' []
./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 block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:739: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:739: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:739: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:751: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:751: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:844: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:844: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:876: 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:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:880: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:880: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:880: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:880: 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:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:905: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:905: 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:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:912: 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:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:961: Warning: line too long
./Tutorial/chapter_searchio.tex:968: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:968: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:995: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:998: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:998: 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:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1005: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1006: 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:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1018: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1019: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1019: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1019: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1019: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1020: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1020: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1020: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1020: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1022: 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:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1026: 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:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1052: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1052: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1076: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1076: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1077: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1077: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1082: Warning: Undefined label: 'sec:SeqIO-index'
./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:1086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1125: 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:1133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1134: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1148: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1158: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1170: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1170: 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:234: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:297: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:300: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:300: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:321: 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 label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:323: Warning: Undefined label: 'sec:efetch'
./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:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:415: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:415: 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:417: Warning: Undefined label: 'chapter:seqio'
./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:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:479: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./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 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-webenv'
./Tutorial/chapter_entrez.tex:486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:499: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:562: Warning: Undefined label: 'sec:elink-citations'
./Tutorial/chapter_entrez.tex:568: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:775: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:777: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:777: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:897: Warning: Undefined label: 'sec:entrez-webenv'
./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:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:943: Warning: line too long
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:985: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:994: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1002: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1025: 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:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1040: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1040: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1058: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1061: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1065: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1078: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1078: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1108: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1152: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1154: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1206: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1241: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1248: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:1249: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1301: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:1325: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_entrez.tex:1326: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1386: Warning: Undefined label: 'sec:entrez-search-fetch-genbank'
./Tutorial/chapter_entrez.tex:1387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1395: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1395: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1496: Warning: Undefined label: 'sec:entrez-and-medline'
./Tutorial/chapter_entrez.tex:1496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1501: Warning: Undefined label: 'sec:elink'
./Tutorial/chapter_entrez.tex:1525: 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:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:247: 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:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:314: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:314: 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:316: 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:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:341: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:343: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:362: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:442: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:442: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:491: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:491: 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:85: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:87: 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:115: 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: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:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:119: 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:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:126: 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:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:276: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:285: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:289: Warning: Image in text
./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:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:358: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:392: 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:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:422: Warning: Undefined label: 'sec:hetero_problems'
./Tutorial/chapter_pdb.tex:467: Warning: Undefined label: 'sec:point_mutations'
./Tutorial/chapter_pdb.tex:484: Warning: Undefined label: 'sec:disordered_atoms'
./Tutorial/chapter_pdb.tex:593: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:607: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:611: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:647: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:658: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:684: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:769: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:769: 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:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:970: Warning: Undefined label: 'table:ic-attribs'
./Tutorial/chapter_pdb.tex:992: Warning: overfull line in array : array too wide
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:992: Warning: line too long
./Tutorial/chapter_pdb.tex:1015: Warning: Undefined citation: 'golub1989'
./Tutorial/chapter_pdb.tex:1043: Warning: Undefined citation: 'hamelryck2005'
./Tutorial/chapter_pdb.tex:1078: Warning: Undefined label: 'table:DSSP-codes'
./Tutorial/chapter_pdb.tex:1118: Warning: Undefined label: 'sec:residue_depth'
./Tutorial/chapter_pdb.tex:1121: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1169: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_pdb.tex:1183: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1380: Warning: Undefined citation: 'hamelryck2003b'
./Tutorial/chapter_pdb.tex:1381: 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:104: Warning: Image in text
./Tutorial/chapter_phylo.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:186: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:186: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:192: Warning: Undefined label: 'fig:phylo-color-draw'
./Tutorial/chapter_phylo.tex:199: Warning: Image in text
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:256: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:256: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:268: 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:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:293: 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:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:346: Warning: line too long
./Tutorial/chapter_phylo.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:360: Warning: Image in text
./Tutorial/chapter_phylo.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:482: 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:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:508: 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:571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:576: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:576: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:607: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:607: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:628: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:628: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:700: 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:715: Warning: Undefined label: 'sec:alignment-tools'
./Tutorial/chapter_phylo.tex:786: 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:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:137: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:164: Warning: Undefined citation: 'cornish1985'
./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cavener1987'
./Tutorial/chapter_motifs.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:209: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:209: 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:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:256: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:256: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:500: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:541: Warning: Undefined citation: 'bailey1994'
./Tutorial/chapter_motifs.tex:549: Warning: line too long
./Tutorial/chapter_motifs.tex:551: Warning: line too long
./Tutorial/chapter_motifs.tex:557: Warning: line too long
./Tutorial/chapter_motifs.tex:559: Warning: line too long
./Tutorial/chapter_motifs.tex:568: Warning: line too long
./Tutorial/chapter_motifs.tex:572: Warning: line too long
./Tutorial/chapter_motifs.tex:574: Warning: line too long
./Tutorial/chapter_motifs.tex:583: Warning: line too long
./Tutorial/chapter_motifs.tex:585: Warning: line too long
./Tutorial/chapter_motifs.tex:586: Warning: line too long
./Tutorial/chapter_motifs.tex:588: Warning: line too long
./Tutorial/chapter_motifs.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:602: 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:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:619: 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:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:687: Warning: Undefined citation: 'matys2003'
./Tutorial/chapter_motifs.tex:709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:711: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:711: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:746: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:746: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:756: 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:771: Warning: Undefined label: 'table:transfaccodes'
./Tutorial/chapter_motifs.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:778: 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:802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:809: 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:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:907: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:907: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:959: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:959: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1043: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1043: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1064: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1064: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1081: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1092: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1092: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1092: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1092: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1101: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1101: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1108: 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:1166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1166: 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:1188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1188: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1312: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1312: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1464: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1496: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1512: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1512: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1529: 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:1564: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: 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:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:234: 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: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: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: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: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:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:259: 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: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: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:270: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:270: 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:276: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:276: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:276: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:276: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: 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: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:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:317: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:329: 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: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: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: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: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:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:340: 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:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:343: 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: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 label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:346: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:346: 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: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: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: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:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:383: 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: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: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:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:418: 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:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:422: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:512: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:512: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:514: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:514: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:518: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:518: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:520: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:520: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:538: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:538: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:540: 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: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: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: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:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:549: 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:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:582: 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:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:586: 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:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:599: Warning: Undefined citation: 'kohonen1997'
./Tutorial/chapter_cluster.tex:599: Warning: Undefined citation: 'tamayo1999'
./Tutorial/chapter_cluster.tex:606: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:610: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:615: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:624: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:624: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:633: 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: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: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: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:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:641: 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:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:645: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:653: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:653: 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:654: 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:654: 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:654: 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:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:659: Warning: Undefined citation: 'yeung2001'
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined citation: 'golub1971'
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:667: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:674: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:674: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:676: 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:682: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:682: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:685: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:689: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:691: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:710: Warning: line too long
./Tutorial/chapter_cluster.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:712: Warning: Undefined block in text mode: 'CODE' []
./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:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:747: Warning: overfull line in array : array too wide
./Tutorial/chapter_cluster.tex:747: Warning: line too long
./Tutorial/chapter_cluster.tex:747: Warning: line too long
./Tutorial/chapter_cluster.tex:753: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:753: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:760: 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:765: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:765: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:766: 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:769: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:769: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:769: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:769: 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:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:772: 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:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:778: 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:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:781: 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:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:798: 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 label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:803: Warning: Undefined label: 'sec:distancematrix'
./Tutorial/chapter_cluster.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:814: 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: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: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: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:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:821: Warning: Undefined label: 'sec:clustercentroids'
./Tutorial/chapter_cluster.tex:830: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:830: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:830: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:830: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:831: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:831: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:831: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:831: 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:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:838: 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:843: 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:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:844: Warning: Undefined label: 'sec:distancefunctions'
./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 block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: 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:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:858: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:859: 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:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:864: 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:868: 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:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:869: Warning: Undefined label: 'sec:distancefunctions'
./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 block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:884: 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:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:887: 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: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:893: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:893: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:894: 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:897: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:897: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:897: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:897: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:901: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:911: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:911: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:911: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:911: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:912: 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: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:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:916: 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: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:920: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:923: 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:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:928: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:940: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:940: 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:942: 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: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:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:950: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:950: 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:952: Warning: Undefined citation: 'hihara2001'
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:969: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:984: 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:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:212: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:212: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:274: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:274: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:276: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:276: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:286: Warning: Undefined label: 'sec:LogisticRegression'
./Tutorial/chapter_learning.tex:290: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined label: 'sec:LogisticRegressionTraining'
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:298: 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:302: 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:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:408: Warning: Application of '\"' on 'i' failed
./Tutorial/chapter_learning.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:418: 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:229: Warning: Optional argument to \item in itemize environment
./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_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:199: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:199: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:204: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./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 block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:206: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:250: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:250: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:324: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:324: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:332: 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:335: 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:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:336: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_cookbook.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:355: 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:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:395: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:395: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:441: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:450: Warning: line too long
./Tutorial/chapter_cookbook.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:452: Warning: Undefined block in text mode: 'CODE' []
./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:455: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:458: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:458: 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:478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:478: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:478: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_cookbook.tex:559: Warning: line too long
./Tutorial/chapter_cookbook.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:591: Warning: Undefined block in text mode: 'CODE' []
./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:641: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_cookbook.tex:653: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:684: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:693: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:693: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:713: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:713: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:713: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:713: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:763: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:763: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:763: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:763: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:765: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:765: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:800: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:803: Warning: line too long
./Tutorial/chapter_cookbook.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:822: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:824: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_cookbook.tex:825: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:825: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:838: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:838: 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:1021: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_cookbook.tex:1028: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1028: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1038: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1050: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1091: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1091: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1124: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1158: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1158: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1206: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1260: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1260: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1336: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1336: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1336: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1358: Warning: line too long
./Tutorial/chapter_cookbook.tex:1359: Warning: line too long
./Tutorial/chapter_cookbook.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1407: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1413: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1416: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1420: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1431: Warning: Undefined label: 'sec:consensus'
./Tutorial/chapter_cookbook.tex:1432: Warning: Undefined label: 'sec:pssm'
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined label: 'sec:getting_info_content'
./Tutorial/chapter_cookbook.tex:1434: Warning: Undefined label: 'sec:sub_matrix'
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1486: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1533: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1560: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1579: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1579: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1612: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1621: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1635: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_cookbook.tex:1637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1696: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1736: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1741: 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_advanced.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:36: Warning: Undefined label: 'sec:substitution_matrices'
./Tutorial/chapter_advanced.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:50: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:50: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:64: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:64: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:162: Warning: Undefined label: 'sec:freq_table'
./Tutorial/chapter_advanced.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:222: Warning: '_' occurring outside math mode
./Tutorial/chapter_advanced.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:234: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:254: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_advanced.tex:254: 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:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:85: Warning: Undefined label: 'chapter:testing'
./Tutorial/chapter_contributing.tex:101: 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:127: Warning: line too long
./Tutorial.tex:138: Warning: Application of '\'' on 'e' failed
./Tutorial.tex:138: Warning: Application of '\'' on 'o' failed
./Tutorial.tex:142: Warning: Application of '\"' on 'u' failed
./Tutorial.tex:216: Warning: Application of '\"' on 'o' failed
./Tutorial.tex:216: Warning: Application of '\"' on 'u' failed
Fixpoint reached in 2 step(s)
pdflatex --shell-escape "\def\bpversion{1.79}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2021-06-01> patch level 1
L3 programming layer <2021-08-27> (./Tutorial.tex
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2021/02/12 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/generic/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.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/tools/calc.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/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.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/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))
(/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))
Excluding 'htmlonly' comment. Excluding 'rawhtml' comment. [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map} <./images/biopython_logo.pdf>]pdfTeX warning 
(ext4): destination with the same identifier (name{page.1}) has been already us
ed, 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-pyg-prefix.pygstyle)
(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/5B3FAD3A26A9987B2E21C41A827DC1CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [4 <./images/biopython_logo_old.jpg>]

LaTeX Warning: Reference `sec:seq-comparison' on page 5 undefined on input line
 186.


Overfull \hbox (2.99303pt too wide) in paragraph at lines 188--190
\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 192.

[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/C083BA757ADC0A392BD8802D1351612C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [7])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.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/AD9EF2BC42CEF4E413923F9BFFE1BE070C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B021334678185567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [9])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F267B6D4EEEA70E83368C1BFCE3E2
2EA7D.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/674F0422DD30F7C4B4E808093732659367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/55B4E33A5EF0F1A0B51702F25755DA0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [12]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/533611943FA3AA7E144BE9661F0999DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/99F306D6A0BEAEBD98D7199579E70E7A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:mutable-seq' on page 13 undefined on input line 8
5.


(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E9762250467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [13])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D938642067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-format' on page 14 undefined on input l
ine 154.


LaTeX Warning: Reference `chapter:seqio' on page 14 undefined on input line 156
.


(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C27067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/06A7ACEFB26AA7DD59C8205B22EBC3D967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [14])
(./_minted-Tutorial/8FDF9BC99C1716A778F3C36AB623FB7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D39467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [15])
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF1767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 16 undefined on
 input line 268.


(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C875367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [16])
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B38667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:seq-module-functions' on page 17 undefined on inp
ut line 343.


(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [17])
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF8267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD6467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF9867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/183C1BBBB8FD6ED15EF6C8F03298A19767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B5599067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO-translate' on page 18 undefined on input li
ne 457.


LaTeX Warning: Reference `sec:seq-module-functions' on page 18 undefined on inp
ut line 463.

[18]
(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [19])
(./_minted-Tutorial/06DBC59F2EAD33E7A95188853787661567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:seq-to-string' on page 20 undefined on input line
 586.

[20]
(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C33867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE45167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [21])
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:seq-to-string' on page 22 undefined on input line
 683.


(./_minted-Tutorial/8009655B8BB14028E5E1BDE9BD4B27E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1107FF2DF5C0B4B87F12506011FBD20867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [22])
(./_minted-Tutorial/6BB61362276E8D90F0EB6BF36B274A6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 23 undefined on input line 744
.


(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [23] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

LaTeX Warning: Reference `chapter:seq_objects' on page 24 undefined on input li
ne 4.


LaTeX Warning: Reference `chapter:seqio' on page 24 undefined on input line 4.


(./_minted-Tutorial/B805770413E9199C6B5EFC63A944737F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seq_objects' on page 24 undefined on input li
ne 21.


LaTeX Warning: Reference `chapter:seqio' on page 24 undefined on input line 21.



LaTeX Warning: Reference `sec:FASTQ-filtering-example' on page 24 undefined on 
input line 34.

[24]

LaTeX Warning: Reference `sec:seq_features' on page 25 undefined on input line 
38.


LaTeX Warning: Reference `chapter:seqio' on page 25 undefined on input line 48.



(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D40767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [25])
(./_minted-Tutorial/510764EE0BB38AD6C688E719896775070C640781732628151051B15D85C
9070A.pygtex)

LaTeX Warning: Reference `chapter:quick_start' on page 26 undefined on input li
ne 131.


LaTeX Warning: Reference `chapter:seqio' on page 26 undefined on input line 133
.


(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D84982267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD208567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D90C640781732628151051B15D85C
9070A.pygtex [26])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A0C640781732628151051B15D85C
9070A.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 27 undefined on input line 212
.


(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA60167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [27])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F92667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:seq_features' on page 28 undefined on input line 
276.


LaTeX Warning: Reference `sec:locations' on page 28 undefined on input line 285
.


LaTeX Warning: Reference `sec:locations' on page 28 undefined on input line 293
.

[28] [29]
(./_minted-Tutorial/2D75ABBC1FC42B7382049A62E37C0E4D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [30])
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/269F8765456CC9B88BDF6A41BC90473E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5B76E9A877CC1A76394FE84519866D4467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [31])

LaTeX Warning: Reference `sec:locations' on page 32 undefined on input line 525
.


(./_minted-Tutorial/18A924CDEFC2ADA66753F94C892F56B167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F9C8B11D1FC2422B35CE8DD6A855273967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B4967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C7567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/86F990EF8173435624D9A400AC90995967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [32])
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E392067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:seq-comparison' on page 33 undefined on input lin
e 627.


LaTeX Warning: Reference `sec:locations' on page 33 undefined on input line 635
.


(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [33])
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F968967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 34 undefined on input line 675
.


LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 34 undefined on i
nput line 678.


(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B234067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [34])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [35])
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A8567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/186CFAEA86C7F6492ED0972D7BC46FE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D245767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-format' on page 36 undefined on input l
ine 820.


(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF8267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:FASTQ-slicing-off-primer' on page 36 undefined on
 input line 832.


LaTeX Warning: Reference `sec:FASTQ-slicing-off-adaptor' on page 36 undefined o
n input line 833.

[36]

LaTeX Warning: Reference `chapter:seqio' on page 37 undefined on input line 846
.


(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF171850166967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [37])
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [38]
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B879367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [39] (./Tutorial/chapter_seqio.tex
Chapter 5.

LaTeX Warning: Reference `chapter:quick_start' on page 40 undefined on input li
ne 4.


LaTeX Warning: Reference `chapter:seq_annot' on page 40 undefined on input line
 4.


(./_minted-Tutorial/DBAB0A8061EF77EEA47B4AA55BAA583C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seq_annot' on page 40 undefined on input line
 13.


LaTeX Warning: Reference `chapter:seq_objects' on page 40 undefined on input li
ne 13.


LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 40 undefined on in
put line 15.


LaTeX Warning: Reference `sec:SeqIO_Online' on page 40 undefined on input line 
23.


LaTeX Warning: Reference `sec:appendix-handles' on page 40 undefined on input l
ine 23.


(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB67814FA033DCB1376922271CBD58A8
A4A36.pygtex [40])

LaTeX Warning: Reference `sec:sequence-parsing' on page 41 undefined on input l
ine 44.


(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE50095414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:sequence-parsing-plus-pylab' on page 41 undefined
 on input line 69.


(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F114FA033DCB1376922271CBD58A8
A4A36.pygtex [41])
(./_minted-Tutorial/C82398A4A04383A063D2E6488112305214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC049107360C640781732628151051B15D85C
9070A.pygtex) [42]

LaTeX Warning: Reference `chapter:seq_annot' on page 43 undefined on input line
 151.


(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C260C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD16222114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD8214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [43])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E7345114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC3950C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE070C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/693D94A81EEABF91A72754E60DEB360614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/AD214E544DAF411AB89A7DCBECDEFFD10C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/E5529B4EE3E3DFEBAAC551606BEAEC6114FA033DCB1376922271CBD58A8
A4A36.pygtex [44])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C9167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:writing-sequence-files' on page 45 undefined on i
nput line 310.


(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:appendix-handles' on page 45 undefined on input l
ine 333.


(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [45])
(./_minted-Tutorial/AFDE811EFDEDCFD9BBD0CAA9BF7F35C267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C0967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO-index-bgzf' on page 46 undefined on input l
ine 401.


LaTeX Warning: Reference `sec:efetch' on page 46 undefined on input line 417.

[46]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD47614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E42159900C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D714FA033DCB1376922271CBD58A8
A4A36.pygtex [47])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D0C640781732628151051B15D85C
9070A.pygtex)

LaTeX Warning: Reference `chapter:entrez' on page 48 undefined on input line 50
7.


LaTeX Warning: Reference `sec:entrez-guidelines' on page 48 undefined on input 
line 507.


LaTeX Warning: Reference `chapter:uniprot' on page 48 undefined on input line 5
12.


(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA60C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/3A5DDBC5C437B752848EE8AB449D41AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [48])

LaTeX Warning: Reference `sec:seqio_todict' on page 49 undefined on input line 
568.


LaTeX Warning: Reference `sec:SeqIO-index' on page 49 undefined on input line 5
74.


LaTeX Warning: Reference `sec:SeqIO-index-db' on page 49 undefined on input lin
e 578.


LaTeX Warning: Reference `sec:SeqIO-indexing-discussion' on page 49 undefined o
n input line 581.


LaTeX Warning: Reference `sec:SeqIO-index' on page 49 undefined on input line 5
91.


(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [49])
(./_minted-Tutorial/A1A806B513EE80294615F1F6C56CA22F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F0C640781732628151051B15D85C
9070A.pygtex)

LaTeX Warning: Reference `sec:fasta-parsing' on page 50 undefined on input line
 665.


(./_minted-Tutorial/1075DB6AF9E4A3F207521105E503858714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB814FA033DCB1376922271CBD58A8
A4A36.pygtex [50])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E830C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/53F70E2F1CBA6BCBDCE4071375628CF767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [51]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C7867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF406567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A36467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:fastq-indexing' on page 52 undefined on input lin
e 786.


(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:seqio-todict-functionkey' on page 52 undefined on
 input line 807.


(./_minted-Tutorial/6209F8400B12665DC9E51BC20774DF7014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [52])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 851--856
\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/D52DA4EEEEE2BF0FBE89EE253714929D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO-sort' on page 53 undefined on input line 86
9.


Overfull \hbox (4.48064pt too wide) in paragraph at lines 894--897
[]\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/D41A88D88AB398F0C3B719A5C7D017C16EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex [53])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E4106EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:seqio-index-getraw' on page 54 undefined on input
 line 951.


(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A277767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [54]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C647167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [55]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD734214FA033DCB1376922271CBD58A8
A4A36.pygtex [56])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C60C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D40C640781732628151051B15D85C
9070A.pygtex [57])

LaTeX Warning: Reference `sec:seqio-index-getraw' on page 58 undefined on input
 line 1192.


(./_minted-Tutorial/C194E2231D844AE7D0223173D2A8999114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/67EFA0AEA2A7C63922644A13FBF91A3767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO-fastq-conversion' on page 58 undefined on i
nput line 1236.


LaTeX Warning: Reference `sec:SeqIO-fasta-qual-conversion' on page 58 undefined
 on input line 1236.

[58]

LaTeX Warning: Reference `sec:seq-reverse-complement' on page 59 undefined on i
nput line 1251.


(./_minted-Tutorial/F1D514FF0D281415CACA329B41D1275667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 59 undefine
d on input line 1261.


(./_minted-Tutorial/218C0A230BCAE3B7E030880B471BA86367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AA1E8DC650125C8460BF37E380CAC1AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1435F1CEA90A4D217A423340747F87F067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CA5B97CA60402CA0078F215AFF31799567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO-translate' on page 59 undefined on input li
ne 1303.


(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA14FA033DCB1376922271CBD58A8
A4A36.pygtex [59])

LaTeX Warning: Reference `sec:SeqRecord-format' on page 60 undefined on input l
ine 1323.


(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F5314FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1341--1343
\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(...)

(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [60]
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1385--1389
[]\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/D3AF6542680CA390CDA8C8DF87C693D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:cookbook' on page 61 undefined on input line 
1404.


(./_minted-Tutorial/D749A84299CF58E876E9A899069830DB14FA033DCB1376922271CBD58A8
A4A36.pygtex)) [61] (./Tutorial/chapter_align.tex
Chapter 6.

LaTeX Warning: Reference `sec:appendix-handles' on page 62 undefined on input l
ine 31.


LaTeX Warning: Reference `sec:AlignIO-count-argument' on page 62 undefined on i
nput line 35.


(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF420C640781732628151051B15D85C
9070A.pygtex [62])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [63])

LaTeX Warning: Reference `sec:alignment-format' on page 64 undefined on input l
ine 113.


(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A3107767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F20C640781732628151051B15D85C
9070A.pygtex) [64]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C56040767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD3310C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B445330C640781732628151051B15D85C
9070A.pygtex [65])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF75667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE0C640781732628151051B15D85C
9070A.pygtex) [66]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A140C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF0200C640781732628151051B15D85C
9070A.pygtex [67])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C50C640781732628151051B15D85C
9070A.pygtex) [68]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D31867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A237144770C640781732628151051B15D85C
9070A.pygtex [69])
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 70 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/9776F24C4F96F850E549BEF997E4D18C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F402467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F0C640781732628151051B15D85C
9070A.pygtex [70])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF1890C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF990C640781732628151051B15D85C
9070A.pygtex [71])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F1614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F560C640781732628151051B15D85C
9070A.pygtex [72])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqRecord-format' on page 73 undefined on input l
ine 633.


(./_minted-Tutorial/2590B11C695B984E246A0A91734F786C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [73]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [74])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B7169267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB0067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E5967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [75])

LaTeX Warning: Reference `sec:SeqRecord-addition' on page 76 undefined on input
 line 813.


(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A925367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34725A02F7895E565E5A29E2AC23E8B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E139611EBF30A11F71B774B00CB422D667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [76]
(./_minted-Tutorial/1FE6956CA319233DB7A5C00C9BEC6D4367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:subs_mat_ex' on page 77 undefined on input line 8
92.


(./_minted-Tutorial/523928538FA511A925EC995B1803BD1667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:pairwise' on page 77 undefined on input line 915.


[77]

LaTeX Warning: Reference `chapter:seqio' on page 78 undefined on input line 919
.


(./_minted-Tutorial/7D984F47D0B3A0329DBE2A791B527F5367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:emboss-needle-water' on page 78 undefined on inpu
t line 949.


(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E89367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C6306467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [78])
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A44267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F98636867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [79])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:phylo' on page 80 undefined on input line 109
5.


(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B04567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/544A0904C171F7ACED98D10D90A2BBA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1128--1132
[]\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/008DB28D2F01F3F29F1F82EB0591003367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AE24E0D965703AA4106AE5CF699F0A9A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [80])
(./_minted-Tutorial/801A8AB951B5DA791C92C02EB6139DB567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/80957FF2744A858A2D626820D87665F167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [81])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E745467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C4AEB9BD8A76F10ACD8C01403E911E8C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/512DFE88FFA610D4550AF5A23966733167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [82]
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:appendix-handles' on page 83 undefined on input l
ine 1316.


(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A24067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [83]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC72660C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/798933B773DD1AAF5C2DC54E06491DCF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/44B6EBA222E5AE2CF0E223148840D8AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF38567467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4988824A3CF97A3309EED328C1CB00D167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [84])
(./_minted-Tutorial/DF151703751D72BD556402B910190A8767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA8867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) [85]
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3B28841A01F9F481844677E14CA7D2A367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2203C1F3E2BE8BEF505556D02F8F382C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F209167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [86])
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [87])
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `durbin1998' on page 88 undefined on input line 1688.


Overfull \hbox (0.78606pt too wide) in paragraph at lines 1686--1689
\OT1/cmr/m/n/10 The new [][]\OT1/cmtt/m/n/10 Bio.Align.PairwiseAligner []\OT1/c
mr/m/n/10 im-ple-ments the Needleman-Wunsch, Smith-Waterman, Go-toh (three-

(./_minted-Tutorial/554024580088332FAF0EA9296BACE82E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:pairwise-aligner' on page 88 undefined on input l
ine 1701.


(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E36167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0ED9274F8C36E3C47BA70FD5BADC364467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [88])
(./_minted-Tutorial/A6265A24C74E31AABCC4CBCDC431287F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71831DAF6DA69540332844566CA78C5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `waterman1987' on page 89 undefined on input line 1774.



(./_minted-Tutorial/E5E00F47BD7A0C8BC5F881852628386867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [89])

LaTeX Warning: Reference `sec:pairwise-substitution-scores' on page 90 undefine
d on input line 1804.


LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 90 undefined o
n input line 1804.


LaTeX Warning: Reference `sec:pairwise-general-gapscores' on page 90 undefined 
on input line 1804.


LaTeX Warning: Reference `sec:pairwise-basic' on page 90 undefined on input lin
e 1805.


LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 90 undefined o
n input line 1808.


LaTeX Warning: Reference `sec:pairwise-general-gapscores' on page 90 undefined 
on input line 1809.


(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE0467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `altschul1990' on page 90 undefined on input line 1835.



LaTeX Warning: Reference `sec:pairwise-affine-gapscores' on page 90 undefined o
n input line 1835.


(./_minted-Tutorial/0EDAB1611DCCA854E910FF7DD9D639FA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [90])
(./_minted-Tutorial/F08297D25DBB0EC458EEDF5510780E9567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `altschul1990' on page 91 undefined on input line 1864.



(./_minted-Tutorial/3DC3D3FA19AFC359663B271CAF187B4867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/17CE58BCB76575958EE7A76C89836E6967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [91])
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1903--1907
[]\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 1903--1907
[]\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: Reference `table:align-meta-attributes' on page 92 undefined on 
input line 1968.


Overfull \hbox (32.852pt too wide) in paragraph at lines 1972--2016
[][]
[92]
(./_minted-Tutorial/52E7DD48238DDBFB9DE1318A616EEA0467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:pairwise-examples' on page 93 undefined on input 
line 2058.


(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE191167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [93] [94])
(./_minted-Tutorial/9EAAC9128F41783D91F19053824A0E3267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB867167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8AC2E9641A86FDB767AE88F57311BBC267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [95])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9680AE27F087032C33AE5BA458DF8E9C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D0167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6C96493DCAF9B522114CF4E5E2ED59EF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [96]
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A3429659267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5F255D6E493419E5F523F2A975278067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E2D8402A42C488B43E823D056683EE7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C93EE09C24214EFB103597E967BC093E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AD99642E498E0D36D353C8D0E91819C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [97])
(./_minted-Tutorial/147547C6C0B329E642CE7584B58DDCED67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0F1FEB8757C2ABBEFF5A5933C033854A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C2A81981348FC122290D4BF339EF28067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [98])
(./_minted-Tutorial/0D2A1E880F29600B639B45481855F3CF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F1B1BD63B0E1791A94C1591A879316E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E0CC5559A1B54F1DFFC0C95E9F657BC967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C3A68CFDB89C0C63A10B21CD7364FEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [99]
(./_minted-Tutorial/6A00D4BA65DCCBE19BE0A5C25F13423067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [100]
(./_minted-Tutorial/7808362E1897955C4D84B6A5C725B37067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/082EF6E387B649F7F6B9332ECA3C14FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C8E736723204677A93FE4D75F2EB836567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E1F81118C07022DC3AE1F5936BE043AA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57D2FD508C41C176AD7A00FFAD0280C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `kent2002' on page 101 undefined on input line 2486.


(./_minted-Tutorial/3363B2217CB2D6762D6F05CF96CEB6EB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [101]
(./_minted-Tutorial/6AFB7518828CB5CE2786BB1F05FA196667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A2CB6704BA931CF6F3C30DE5475D088D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [102])
(./_minted-Tutorial/F4D1EFD0A75F8F251D61853DB5B12A7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94D69571A69F80E3CCD32B0AFD10CBB467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E624B311569CC6FAA91D2E8671D827FB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [103])
(./_minted-Tutorial/7442AA52B0FC887EC2AAC73A4E59FFFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA7767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [104])
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF79660067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2671--2672
\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/F89522EF58FB067C6521C367C713471667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE2067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71A68A4BDF8B5654D3E2E0470AE163B467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CE4E999FF33F9D09A2BB895447AA462967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [105]
(./_minted-Tutorial/3E4691AEB06522E457CDE497E3092DE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `schneider2005' on page 106 undefined on input line 276
3.


LaTeX Warning: Reference `sec:substitution_matrices' on page 106 undefined on i
nput line 2763.


(./_minted-Tutorial/2E1DF2678D7C68CA2C465BCE6BBBBD6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C149B172A838F697839B85AE70CC6CDB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [106])
(./_minted-Tutorial/467CA50C36874E405E988587FEC0768667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/819EB88A2CBCC7948E4BEBE7FB9F80EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22DC4F8C7ADBE16392AA93A6EF2819D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/171A69BE62E368AD65396E23A20B1DEE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A1C712272F319372A1AB78DEB403D23367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [107])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A7367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [108])
(./_minted-Tutorial/F31773576B5C3B14C8BCFC3D71E2671467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [109])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E656D3A6BB3675CEC995C2C398DA729367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31A4214F0316300852C263796C130BE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [110])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AB42E81B0039139237BF82BA22516C8B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F45B7CF5E8DCF44722DA12A77C5BD96967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/256D8F4D1BB7E6301923B808B6EEB34567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7AFBDEDDA8F411FC4281444B70E6021E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [111])
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE313567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9730D42326723F9A4A3771D68D644E7C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E3A6838E914945B67D684750F42B90B267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [112])
(./_minted-Tutorial/A117079E905A3317941FA3CB9457C22567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA82527867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F68009367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [113])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/54D7EA4835796C5C4162263077D6191C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D8624166470767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B50C640781732628151051B15D85C
9070A.pygtex [114])
(./_minted-Tutorial/BCCC189D6984A3CAE23757DF96064B4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DFB937A17182FF8FB5EABF3F70A58B0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `altschul1990' on page 115 undefined on input line 3319
.


(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D0C640781732628151051B15D85C
9070A.pygtex [115])
(./_minted-Tutorial/4DC21B98C2C48E89E7C16C6BAB13C5CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9ED67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A29DE03FF59071EADD7632CC7B11243E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [116])

LaTeX Warning: Citation `henikoff1992' on page 117 undefined on input line 3391
.


LaTeX Warning: Citation `dayhoff1978' on page 117 undefined on input line 3391.



(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5D9F7C1083DA643BDA1083E79D82EF2067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `schneider2005' on page 117 undefined on input line 341
5.


(./_minted-Tutorial/20711981BAB695B8006B7A92E4859CF667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [117] (./Tutorial/chapter_blast.tex
Chapter 7.

LaTeX Warning: Reference `chapter:searchio' on page 118 undefined on input line
 18.

[118]

LaTeX Warning: Reference `sec:parsing-blast' on page 119 undefined on input lin
e 58.


(./_minted-Tutorial/04BEBF413314D7A51FC0F91D3066CE4F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 119 undefined on input line 11
9.


LaTeX Warning: Reference `sec:parsing-blast' on page 119 undefined on input lin
e 124.


(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [119])

LaTeX Warning: Reference `sec:parsing-blast' on page 120 undefined on input lin
e 146.


(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C20467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:parsing-blast' on page 120 undefined on input lin
e 155.


LaTeX Warning: Reference `sec:running-www-blast' on page 120 undefined on input
 line 164.


LaTeX Warning: Reference `sec:alignment-tools' on page 120 undefined on input l
ine 192.


(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/B402706802BF02F25F9B09CDB22A3FEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [120])

LaTeX Warning: Reference `sec:parsing-blast' on page 121 undefined on input lin
e 236.


LaTeX Warning: Reference `sec:running-www-blast' on page 121 undefined on input
 line 286.


LaTeX Warning: Reference `sec:running-local-blast' on page 121 undefined on inp
ut line 288.

[121]

LaTeX Warning: Reference `sec:appendix-handles' on page 122 undefined on input 
line 303.


(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C20467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE521800467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 122 undefined on input line 33
9.


LaTeX Warning: Reference `chapter:align' on page 122 undefined on input line 33
9.


(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F4039467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDFE599DAB8ED6AC4F17D4FC6F0230BC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [122])
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D23867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F90D3141F79DD2447A9059C65E1C6B4367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B19240C640781732628151051B15D85C
9070A.pygtex [123])

LaTeX Warning: Reference `fig:blastrecord' on page 124 undefined on input line 
449.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:psiblastrecord' on page 124 undefined on input li
ne 465.

Excluding 'htmlonly' comment.

LaTeX Warning: Float too large for page by 32.27644pt on input line 478.

) [124] [125 <./images/BlastRecord.png>] [126 <./images/PSIBlastRecord.png>]
(./Tutorial/chapter_searchio.tex
Chapter 8.

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C
9070A.pygtex) [127]
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/0EF47CD31A1F702FF10BD5C95E6D18FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [128])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B5195567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [129])
(./_minted-Tutorial/5218313E7181C19A936D3F4347E1930A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7BE69614D007F3BE3249A547A9661D0767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE32767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [130])
(./_minted-Tutorial/DC6D0E585B2AACAC1C88A760863B4E4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/130BC5013C07805E69A888444A0B34DB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [131]
(./_minted-Tutorial/0E8B9F4E4323CB258CA049D41E4AB7F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAA6FD197F3F78FDFB781210387FEC2667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [132])
(./_minted-Tutorial/67A62206561049F4B7E307FD79F028C967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5E1CC554EC31697163DDD9D33E32A45667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [133])
(./_minted-Tutorial/0A806FC81D8F7F64321B4A6911027F0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [134]
(./_minted-Tutorial/DC76D831C6E940E11ED2C9452F770E0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A61EC24A4603554A3865574A6B7378067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [135]
(./_minted-Tutorial/4D85AB21D9819B066A1C948098FDB54B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE57357767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4D9A79F8BB08FCA20BAEA3DFAAA08BA467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/62792AA2C0390B83FD6A91F3B267312A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [136])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD88044467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C78767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seq_annot' on page 137 undefined on input lin
e 734.


Overfull \hbox (27.24287pt too wide) in paragraph at lines 738--740
[]\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/338C616C7128C3DB7FFD516F5C2BDA1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [137])
(./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [138])
(./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [139]
(./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B41343A9090DC4C41F9EC69AB6DEDE1B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [140]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054
\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/B5F76D201899B345CB64AACD67C7346067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO-index' on page 141 undefined on input line 
1082.


Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085
[]\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/0AB25750C7D89E832295045C60D6B8C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [141])
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E986867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E4B312798560C8CE4ABF272A364D9E2F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/35C0940CA4025285AAECA54EF82C993367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1160--1163
[]\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/BDE985FA3ADA6B0D37013C3D5F37C17667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [142] [143] (./Tutorial/chapter_entrez.tex
Chapter 9.
[144]

LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 145 undefined
 on input line 21.


(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [145]

LaTeX Warning: Reference `sec:entrez-webenv' on page 146 undefined on input lin
e 60.


LaTeX Warning: Reference `sec:BioSQL' on page 146 undefined on input line 63.


(./_minted-Tutorial/7692669934D8ED6DEE1B8B668474542167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [146])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C00867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FAC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [147])
(./_minted-Tutorial/1FE33E4DDF6E596EA7687FB6F017F09967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C6867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:efetch' on page 148 undefined on input line 216.


LaTeX Warning: Reference `sec:entrez-einfo' on page 148 undefined on input line
 220.


(./_minted-Tutorial/A4BD3C61B53064F601B4477CDD3106A667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:efetch' on page 148 undefined on input line 234.


(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [148])
(./_minted-Tutorial/36931D2CFB3ECF0D53B3D7376832300467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/ED23259F6CF56D8483B68EF02BB7325067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 149 undefined on input lin
e 297.

[149]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 150 undefined on in
put line 323.


LaTeX Warning: Reference `sec:efetch' on page 150 undefined on input line 323.


(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F314767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [150] [151])

LaTeX Warning: Reference `chapter:seqio' on page 152 undefined on input line 41
7.


(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D514FA033DCB1376922271CBD58A8
A4A36.pygtex [152])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F48767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 153 undefined
 on input line 479.


LaTeX Warning: Reference `sec:entrez-webenv' on page 153 undefined on input lin
e 481.


(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF00867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [153])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5AB8B67C801B8858B19590FE5D018BA367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:elink-citations' on page 154 undefined on input l
ine 562.


LaTeX Warning: Reference `sec:entrez_example_genbank' on page 154 undefined on 
input line 568.


(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [154])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC3867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E096EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/0290A0C926605EF68EF2EEEAEB078A0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [155])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF380C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E710C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB860C640781732628151051B15D85C
9070A.pygtex) [156]
(./_minted-Tutorial/BE0AC194CA3417BFC49309A9791ED35B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B0C640781732628151051B15D85C
9070A.pygtex [157])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 158 undefined on in
put line 777.


LaTeX Warning: Reference `sec:efetch' on page 158 undefined on input line 777.

[158]
(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/97FFA15DF713393C0351F9F947AC446667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34883991B974FF1C1BE2D18B230693C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [159])
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/079D37C5A2B3943F37FA4CC9C5C43BC767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5056BF2116652C732E1D8E3CDA11D6AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 160 undefined on input lin
e 897.

[160]
(./_minted-Tutorial/4997CC17B3360B104654D2ED20FA8B4067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A126667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F20190C640781732628151051B15D85C
9070A.pygtex [161])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B62467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9C337E8D92F5A543D90F4D2C8BCBF18367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [162])
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA114FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 163 undefined on input line 1065
.


(./_minted-Tutorial/B875C8F385654DD9607A0DAA82B3371067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [163])
(./_minted-Tutorial/F62235DAC4152853E8C6EBBD7E2D286167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 164 undefined on input lin
e 1108.


(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 164 undefined on input line 1154
.

[164]
(./_minted-Tutorial/491F8A9C8CFC3BB4763B296852A6D1D567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F7725E37E412C564C008C3BCECB547CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B64203867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 165 undefined on input lin
e 1206.


(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [165])
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 166 undefined on input lin
e 1241.


LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 166 undefined on in
put line 1248.


LaTeX Warning: Reference `sec:entrez-webenv' on page 166 undefined on input lin
e 1249.


(./_minted-Tutorial/D8F151290BCF14625BA5E4CD26A7FB1E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [166])
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A7279767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB384867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 167 undefined on input line 13
01.


(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4EDDF5C23B0FCCC279960365B499A16C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [167])

LaTeX Warning: Reference `sec:entrez-guidelines' on page 168 undefined on input
 line 1325.


LaTeX Warning: Reference `sec:entrez-webenv' on page 168 undefined on input lin
e 1326.


(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C4567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB9364967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [168]

LaTeX Warning: Reference `sec:entrez-search-fetch-genbank' on page 169 undefine
d on input line 1386.


(./_minted-Tutorial/FE862EFCF9F786EA3C4D97E3821A5CAA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:entrez_example_genbank' on page 169 undefined on 
input line 1407.


(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E2467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F963367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D57414FA033DCB1376922271CBD58A8
A4A36.pygtex [169])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA14FA033DCB1376922271CBD58A8
A4A36.pygtex [170])

LaTeX Warning: Reference `sec:entrez-and-medline' on page 171 undefined on inpu
t line 1496.


LaTeX Warning: Reference `sec:elink' on page 171 undefined on input line 1501.


(./_minted-Tutorial/826A4111F6CE74D7A673B6C8F5681FC367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 171 undefined on input lin
e 1525.


(./_minted-Tutorial/F52B50369F8EBC15506CCA30EE3F873367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [171] (./Tutorial/chapter_uniprot.tex
Chapter 10.

LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 172 undefined
 on input line 12.


(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A8667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A66867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD676867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:expasy_swissprot' on page 172 undefined on input 
line 37.


(./_minted-Tutorial/930B60BD569CAAF368B0E614553F303067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 172 undefined
 on input line 45.

[172]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA651918267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/68D834E8AB9E722FD7953C65DB7E9FDB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD6922867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D1467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [173])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A451791867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF256282240C640781732628151051B15D85C
9070A.pygtex [174])
(./_minted-Tutorial/3876A0F1CD2CBCD824C73B244059EE4767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [175])
(./_minted-Tutorial/7A92C6B39F0BC9AE063090BDDCD011DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B0C640781732628151051B15D85C
9070A.pygtex [176])
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC78367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [177]
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 178 undefined on input line 343.



(./_minted-Tutorial/3C3B5BB472E9A4A7B3F5BFA41CA60C7867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (24.29903pt too wide) in paragraph at lines 362--363
[]\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/483E7285F7FA2A76D28505EE0DE792D467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [178])
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 405--406
[]\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/DF2DA17EFC0F6336210C74066809B75367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9457A436D281E066D350873A88476E5967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [179])
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A80C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AB8625F199818648FAC2C5737C2D032067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [180])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E8616967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [181] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C2285367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E6908567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [182])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA738867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB3567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36B58FEFA589A67048E7D5B63D489DAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB823167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:problem_structures' on page 183 undefined on inpu
t line 85.


(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [183]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E1867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D17667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A02467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [184])
(./_minted-Tutorial/05F3B09A7CBE08B1C91DE55284F12C2867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [185]
Overfull \hbox (13.022pt too wide) in paragraph at lines 263--265
\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)

LaTeX Warning: Reference `fig:smcra' on page 186 undefined on input line 276.


LaTeX Warning: Reference `sec:problem_structures' on page 186 undefined on inpu
t line 285.

Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D97967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [186] [187 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD85567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB24767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E272762267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [188]

LaTeX Warning: Reference `sec:hetero_problems' on page 189 undefined on input l
ine 422.


(./_minted-Tutorial/2F13678C6026DEBF0D98D4214CDF499867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:point_mutations' on page 189 undefined on input l
ine 467.


(./_minted-Tutorial/DE3953D86837855582C4B8B9F38D7FD667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:disordered_atoms' on page 189 undefined on input 
line 484.

[189]
(./_minted-Tutorial/D15D1F955440960DB3C5206BF3EEE29E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/652F2E49D1B3634A04F3CB950B38570467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [190])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC8809867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB1249267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `fig:smcra' on page 191 undefined on input line 611.


(./_minted-Tutorial/84495A3B19FA62DBFC292B309E5DE1E567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [191])

LaTeX Warning: Reference `fig:smcra' on page 192 undefined on input line 658.


(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [192]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB9067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B12867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [193])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF23189967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/87466E9C05D4662C6164A2AFA3A69C4967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC266367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA3967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [194])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E66767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/200193443B83EEADE7971FACFD86F16D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A49EF93DADD431750435FD5125A74A0567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [195])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D51872E4871C96F9D4DDBFAF9C4DF2EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [196]
Overfull \hbox (42.26714pt too wide) in paragraph at lines 953--957
\OT1/cmr/m/n/10 breaks and dis-or-dered residues and atoms as de-scribed above 
are han-dled cor-rectly. \OT1/cmtt/m/n/10 structure[]rebuild[]test(entity)

LaTeX Warning: Reference `table:ic-attribs' on page 197 undefined on input line
 970.


Overfull \hbox (3.8904pt too wide) in paragraph at lines 973--993
[][] 

LaTeX Warning: Citation `golub1989' on page 197 undefined on input line 1015.


(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [197])

LaTeX Warning: Citation `hamelryck2005' on page 198 undefined on input line 104
3.


LaTeX Warning: Command \r invalid in math mode on input line 1046.


(./_minted-Tutorial/0F60C02FB1C0A5EBADB8EF693216594667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `table:DSSP-codes' on page 198 undefined on input line
 1078.


LaTeX Warning: Reference `sec:residue_depth' on page 198 undefined on input lin
e 1118.

[198]
(./_minted-Tutorial/163F04F633C696E8F41EBFFBB74DAF9D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/84DC73903FA70E943C63131089E2ED9F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `hamelryck2003a' on page 199 undefined on input line 11
69.

[199] [200]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB1567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [201]
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [202]

LaTeX Warning: Citation `hamelryck2003b' on page 203 undefined on input line 13
80.


LaTeX Warning: Citation `majumdar2005' on page 203 undefined on input line 1381
.

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

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B115204AFF525DDD4F3CF69B79C0739114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC14FA033DCB1376922271CBD58A8
A4A36.pygtex [204])) [205] (./Tutorial/chapter_phylo.tex
Chapter 13.

LaTeX Warning: Citation `talevich2012' on page 206 undefined on input line 9.


(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC56710C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE1586EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C2467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [206])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `fig:phylo-simple-draw' on page 207 undefined on input
 line 96.


(./_minted-Tutorial/3E6F23F473B4E07E8F7181EEE5B0B4A567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [207]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178
[]\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/29624A9666C9430AABADF395148BBF2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `fig:phylo-color-draw' on page 208 undefined on input 
line 192.


(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [208 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/6382EC6908438B3E67C757E70A11466C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [209 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/6D2EF2116C7B06D5B8D357EA567F832E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A145A6C1AAD034F2FF71DE52310A2BD467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/787FD2B6485DC30362A59A325340738367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F5567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [210])
(./_minted-Tutorial/9DD9A1F0A4FFCEEE15CCB35AFAE0B5FB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7692F6F4FEC56E165A881DE3F8A965167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) Excluding 'htmlonly' comment. [211]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445
\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"})
[212 <./images/phylo-draw-example.png>]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496
[]\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
 ,
[213]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF614FA033DCB1376922271CBD58A8
A4A36.pygtex) [214]
(./_minted-Tutorial/5B477DBF8C94B1E6FDC020E6A741C0DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A317CBB9F004B52870B25AB07ACF279167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (4.04672pt too wide) in paragraph at lines 708--711
[]\OT1/cmr/m/n/10 A sim-i-lar wrap-per for RAxML ([][]$\OT1/cmtt/m/n/10 https :
 / / sco . h-[]its . org / exelixis / software . html$[][]\OT1/cmr/m/n/10 ) was
 added in Biopy-

LaTeX Warning: Reference `sec:alignment-tools' on page 215 undefined on input l
ine 715.

[215]
(./_minted-Tutorial/4A4A0B08C37495B73842BFCD67A687D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [216]

LaTeX Warning: Reference `sec:PhyloXML' on page 217 undefined on input line 786
.

) [217] (./Tutorial/chapter_motifs.tex
Chapter 14.

LaTeX Warning: Reference `sec:links' on page 218 undefined on input line 8.


(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F155F8EF3B63ECD9B6708A42B8F5F72A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [218])
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE7567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D17767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D25717367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/666DFB2D351C7C4DE86ECB38CCBB491867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [219])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F6124319202267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `cornish1985' on page 220 undefined on input line 164.


LaTeX Warning: Citation `cavener1987' on page 220 undefined on input line 165.


(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB247667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [220]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA0C640781732628151051B15D85C
9070A.pygtex [221])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [222])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D140C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C7667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF920C640781732628151051B15D85C
9070A.pygtex [223])
(./_minted-Tutorial/B5E175DBFE536E62D3BB466A47FD029F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [224])
(./_minted-Tutorial/7F5E0E05D69E7F9EC30F2A5CD5D9B5F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [225])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/696A69FC8317D40C8605CBADFDA5D87767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [226]
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6382581C9B01D86887B13EFD1FA7AFA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C37867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C1EF8469C0F4B427273EE106072F9E6667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [227])

LaTeX Warning: Citation `bailey1994' on page 228 undefined on input line 541.


(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F80C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E440C640781732628151051B15D85C
9070A.pygtex [228])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 602--605
\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/147DE2DA7F37C2A5A1C1344033AB8B8467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [229])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E01205367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `matys2003' on page 230 undefined on input line 687.


(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA70C640781732628151051B15D85C
9070A.pygtex [230])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8C09EEE739CAD078852B77A784E1269267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `table:transfaccodes' on page 231 undefined on input l
ine 771.


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


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


(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [231] [232])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F2640667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF5149567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE7060567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [233])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [234])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B3F030F5FA6A7817CFA605062601C81267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E22567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E4867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [235])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8F2A64376DB87D5A7AB48BFE3760B0B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [236])
(./_minted-Tutorial/22387CA0FB9349FBC21B30A09B80342067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A8167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA16167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [237]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E2567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A509267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C8607367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE97067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [238])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [239])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E32267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD726160367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA247367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [240])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA1667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [241]
(./_minted-Tutorial/63EC9F933A4699B71D633AB9C35237C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5032B21DEC5EBE299D472B0AF220432A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A2667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F44720C640781732628151051B15D85C
9070A.pygtex) [242]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [243]) [244] (./Tutorial/chapter_cluster.tex
Chapter 15.

LaTeX Warning: Citation `dehoon2004' on page 245 undefined on input line 6.


LaTeX Warning: Citation `lecuyer1988' on page 245 undefined on input line 30.


LaTeX Warning: Citation `kachitvichyanukul1988' on page 245 undefined on input 
line 30.

[245] [246] [247]

LaTeX Warning: Citation `snedecor1989' on page 248 undefined on input line 154.


[248]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED414067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 249 undefined on input
 line 183.


(./_minted-Tutorial/2CEA2595B9B8CEAD10513E8D15566D0167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE60173582767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A250014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [249])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 244--245
\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/05DC01C08B8EDF71F86E3C3A9C28EB3467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [250]

LaTeX Warning: Reference `sec:distancefunctions' on page 251 undefined on input
 line 277.

[251]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [252]

LaTeX Warning: Reference `sec:distancefunctions' on page 253 undefined on input
 line 345.


(./_minted-Tutorial/C286E2777B917B774560CBDC7CF9262667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8
A4A36.pygtex) [253] [254]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 422--423
[][]\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/015798D317E9D8732518AFD186C997CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C23904926786173967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [255]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE2267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [256]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F7267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF889505567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 257 undefined on input
 line 555.


(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [257])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Citation `kohonen1997' on page 258 undefined on input line 599.


LaTeX Warning: Citation `tamayo1999' on page 258 undefined on input line 599.

[258]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C17567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 259 undefined on input
 line 646.

[259]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 653--655
\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 260 undefined on input line 659.


LaTeX Warning: Citation `golub1971' on page 260 undefined on input line 667.


(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [260]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A7DB1B14B8C3B59B03D102D4BEECDD167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D220C09E8614EBE54BD07A8C18AAC3367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [261]
Overfull \hbox (25.39864pt too wide) in paragraph at lines 737--748
 [] 
[262]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 263 undefined on input
 line 800.


LaTeX Warning: Reference `sec:distancematrix' on page 263 undefined on input li
ne 803.


(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:clustercentroids' on page 263 undefined on input 
line 821.


(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [263]

LaTeX Warning: Reference `sec:distancefunctions' on page 264 undefined on input
 line 844.


(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 264 undefined on input
 line 869.


(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [264]

LaTeX Warning: Reference `sec:distancefunctions' on page 265 undefined on input
 line 898.


(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA850467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 265 undefined on input
 line 920.

[265]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 927--929
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Citation `hihara2001' on page 266 undefined on input line 952.


(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [266])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF5867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 984--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 
. 
[267] (./Tutorial/chapter_learning.tex
Chapter 16.
[268]

LaTeX Warning: Reference `eq:OP' on page 269 undefined on input line 40.


LaTeX Warning: Reference `eq:NOP' on page 269 undefined on input line 40.


LaTeX Warning: Reference `table:training' on page 269 undefined on input line 7
5.


(./_minted-Tutorial/8C8664D7942C9DDA1DE175A432DAD57267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [269])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D87A6F5674B92E17575B5F1479772CA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [270]) [271]
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB09667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `eq:OP' on page 272 undefined on input line 212.


LaTeX Warning: Reference `eq:NOP' on page 272 undefined on input line 212.


(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D40267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94C0A9A9293B19D950018F966B967E8167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [272])
(./_minted-Tutorial/A1B56761C52CC91D59E84159B69EC85E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `eq:OP' on page 273 undefined on input line 274.


LaTeX Warning: Reference `eq:NOP' on page 273 undefined on input line 274.


LaTeX Warning: Reference `eq:OP' on page 273 undefined on input line 276.


LaTeX Warning: Reference `eq:NOP' on page 273 undefined on input line 276.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 280.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 280.

[273]

LaTeX Warning: Reference `sec:LogisticRegression' on page 274 undefined on inpu
t line 286.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 288.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 288.


LaTeX Warning: Reference `table:training' on page 274 undefined on input line 2
90.


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:LogisticRegressionTraining' on page 274 undefined
 on input line 298.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 300.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 300.


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA59567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FF01A8BA64DD59AF7C1265FFBD6C1B5267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/27D68FCC443982B3438F0C03A4D541D667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [274])
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC1567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/10829292EF1E211AEAC19B179A46CD1067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7F43A5B55F7492DFDBA4E17BF7F34F4767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [275])) [276] (./Tutorial/chapter_graphics.tex
Chapter 17.

LaTeX Warning: Citation `pritchard2006' on page 277 undefined on input line 18.



LaTeX Warning: Citation `toth2006' on page 277 undefined on input line 28.


LaTeX Warning: Citation `vanderauwera2009' on page 277 undefined on input line 
31.


LaTeX Warning: Reference `chapter:seq_annot' on page 277 undefined on input lin
e 36.


LaTeX Warning: Reference `chapter:seqio' on page 277 undefined on input line 36
.

[277]

LaTeX Warning: Reference `chapter:seqio' on page 278 undefined on input line 64
.


(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D81614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B03514FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_linear' on page 278 undefined on input li
ne 136.


(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA714FA033DCB1376922271CBD58A8
A4A36.pygtex [278]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_circular' on page 279 undefined on input 
line 167.


(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E14FA033DCB1376922271CBD58A8
A4A36.pygtex [279 <./images/plasmid_linear.png (PNG copy)>])

LaTeX Warning: Reference `sec:seq_features' on page 280 undefined on input line
 220.

[280 <./images/plasmid_circular.png (PNG copy)>]
(./_minted-Tutorial/5D58687CD77437A3DD50DABD32F1536714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/0EA68B85D005018D196EB15C866B9F3814FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_labels' on page 281 undefined on input l
ine 260.


(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D85014FA033DCB1376922271CBD58A8
A4A36.pygtex [281]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_labels' on page 282 undefined on input l
ine 330.


LaTeX Warning: Reference `sec:gd_features_without_seqfeatures' on page 282 unde
fined on input line 339.


LaTeX Warning: Reference `sec:gd_feature_captions' on page 282 undefined on inp
ut line 339.


LaTeX Warning: Reference `sec:gd_features_without_seqfeatures' on page 282 unde
fined on input line 339.


LaTeX Warning: Reference `sec:gd_feature_captions' on page 282 undefined on inp
ut line 339.


LaTeX Warning: Reference `sec:gd_nice_example' on page 282 undefined on input l
ine 345.


(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B9414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C14FA033DCB1376922271CBD58A8
A4A36.pygtex [282] [283 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigils' on page 284 undefined on input line 38
7.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `sec:gd_sigils' on page 284 undefined on input line 40
3.


(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB14FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_arrow_shafts' on page 284 undefined on i
nput line 434.


LaTeX Warning: Reference `sec:gd_arrow_sigils' on page 284 undefined on input l
ine 439.


(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A14FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_arrow_heads' on page 284 undefined on in
put line 463.


LaTeX Warning: Reference `sec:gd_arrow_sigils' on page 284 undefined on input l
ine 468.


(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F14FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Reference `sec:gd_top_down' on page 284 undefined on input line 
488.


(./_minted-Tutorial/0ABDE2E70066A4661C3DDA814AC7225814FA033DCB1376922271CBD58A8
A4A36.pygtex [284] [285 <./images/GD_sigils.png>] [286 <./images/GD_sigil_arrow
_shafts.png>] [287 <./images/GD_sigil_arrow_heads.png>] [288])
Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_linear_nice' on page 289 undefined on inp
ut line 570.


LaTeX Warning: Reference `fig:plasmid_circular_nice' on page 289 undefined on i
nput line 571.


LaTeX Warning: Reference `sec:gd_nice_example' on page 289 undefined on input l
ine 577.


LaTeX Warning: Reference `sec:gd_nice_example' on page 289 undefined on input l
ine 577.


LaTeX Warning: Reference `sec:gd_nice_example' on page 289 undefined on input l
ine 585.


LaTeX Warning: Reference `sec:gd_nice_example' on page 289 undefined on input l
ine 585.


LaTeX Warning: Citation `proux2002' on page 289 undefined on input line 596.


LaTeX Warning: Reference `sec:efetch' on page 289 undefined on input line 605.


LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 289 undefined on input
 line 608.


LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 289 undefin
ed on input line 610.

[289 <./images/plasmid_linear_nice.png (PNG copy)>] [290 <./images/plasmid_circ
ular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA8914FA033DCB1376922271CBD58A8
A4A36.pygtex [291])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177A14FA033DCB1376922271CBD58A8
A4A36.pygtex [292]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:three_track_simple' on page 293 undefined on inpu
t line 732.


LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 293 undefined on inpu
t line 739.


LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 293 undefined on inpu
t line 739.


LaTeX Warning: Citation `proux2002' on page 293 undefined on input line 759.


(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA11114FA033DCB1376922271CBD58A8
A4A36.pygtex [293 <./images/three_track_simple.png>])
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD184014FA033DCB1376922271CBD58A8
A4A36.pygtex [294])
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C2814FA033DCB1376922271CBD58A8
A4A36.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 295 undefined on input li
ne 894.


LaTeX Warning: Reference `sec:gd_cross_links' on page 295 undefined on input li
ne 901.


LaTeX Warning: Reference `sec:gd_cross_links' on page 295 undefined on input li
ne 901.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:three_track_cl2' on page 295 undefined on input l
ine 927.


LaTeX Warning: Reference `sec:gd_cross_links' on page 295 undefined on input li
ne 934.


LaTeX Warning: Reference `sec:gd_cross_links' on page 295 undefined on input li
ne 934.

[295] [296 <./images/three_track_cl.png>] [297 <./images/three_track_cl2a.png>]

(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F72841497714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F14FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Citation `jupe2012' on page 298 undefined on input line 1012.


(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC14FA033DCB1376922271CBD58A8
A4A36.pygtex [298] [299 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])

(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C14FA033DCB1376922271CBD58A8
A4A36.pygtex [300]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:simplechromosome' on page 301 undefined on input 
line 1114.


(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A7514FA033DCB1376922271CBD58A8
A4A36.pygtex [301]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:simplechromosome' on page 302 undefined on input 
line 1194.

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

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [303]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B14FA033DCB1376922271CBD58A8
A4A36.pygtex [304])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C950C640781732628151051B15D85C
9070A.pygtex)) [305] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [306]
(./_minted-Tutorial/F7E0F1384D5EE10CDFEDB2428F50CCC667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB4467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB08167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B6CD5F177651EF61E679B9FAF6C25BE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [307])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D720667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [308])
(./_minted-Tutorial/EE7361AC934053D42AE642DBF97DE34A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [309])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [310] (./Tutorial/chapter_cookbook.tex
Chapter 20.

LaTeX Warning: Reference `chapter:seqio' on page 311 undefined on input line 22
.


(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB14FA033DCB1376922271CBD58A8
A4A36.pygtex [311])

LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 312 undefined on i
nput line 58.


(./_minted-Tutorial/FF8B764D5420CEF9ECE1CDD6385A3BDC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E5716467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [312]
(./_minted-Tutorial/D24532DF36691735DACEF9DD7062845467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 313 undefined on 
input line 146.


(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/54D3F8BEB8094C8ADFFB26585CE1463814FA033DCB1376922271CBD58A8
A4A36.pygtex [313])

LaTeX Warning: Reference `sec:translation' on page 314 undefined on input line 
199.


LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 314 undefined o
n input line 204.


(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F6414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A023964706114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B14FA033DCB1376922271CBD58A8
A4A36.pygtex) [314]
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC6554114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE40879314FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Reference `sec:seqio-index-getraw' on page 315 undefined on inpu
t line 336.


(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D914FA033DCB1376922271CBD58A8
A4A36.pygtex [315])
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA214FA033DCB1376922271CBD58A8
A4A36.pygtex) [316]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF64183114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F3545014FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 317 undefined on i
nput line 441.


LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 317 undefined on i
nput line 455.


Overfull \hbox (5.83499pt too wide) in paragraph at lines 452--456
\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/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (4.57849pt too wide) in paragraph at lines 473--475
\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 317 undefined on input
 line 478.

[317]
(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA55614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A14FA033DCB1376922271CBD58A8
A4A36.pygtex [318])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F891514FA033DCB1376922271CBD58A8
A4A36.pygtex [319])

LaTeX Warning: Reference `sec:SeqIO-conversion' on page 320 undefined on input 
line 641.


LaTeX Warning: Citation `cock2010' on page 320 undefined on input line 644.

[320]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C3114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC4073736714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/8ADDD83BA2CAFB21C875C8B9C0986B9B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B514FA033DCB1376922271CBD58A8
A4A36.pygtex [321])
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A014FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Reference `sec:SeqIO-index' on page 322 undefined on input line 
800.


(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [322]

LaTeX Warning: Reference `sec:SeqIO-index' on page 323 undefined on input line 
822.


LaTeX Warning: Reference `sec:SeqIO-sort' on page 323 undefined on input line 8
24.


LaTeX Warning: Reference `sec:SeqIO-conversion' on page 323 undefined on input 
line 838.


(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/41250203CD471B54840A6F5E1188318D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [323]

LaTeX Warning: Reference `sec:translation' on page 324 undefined on input line 
905.


(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BAE95C3681F5665B01248E86DAC866B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B214FA033DCB1376922271CBD58A8
A4A36.pygtex [324])
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A630520C640781732628151051B15D85C
9070A.pygtex [325])

LaTeX Warning: Reference `sec:gd_nice_example' on page 326 undefined on input l
ine 1021.


LaTeX Warning: Reference `chapter:seqio' on page 326 undefined on input line 10
38.


(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B714FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:seq-len-hist' on page 326 undefined on input line
 1106.

[326]
Overfull \hbox (4.00363pt too wide) in paragraph at lines 1114--1117
[]\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/7C23BDB073E316E7093E4D3A77BD752E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD14FA033DCB1376922271CBD58A8
A4A36.pygtex [327 <./images/hist_plot.png>]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:seq-gc-plot' on page 328 undefined on input line 
1172.


LaTeX Warning: Reference `fig:nuc-dot-plot' on page 328 undefined on input line
 1186.

Excluding 'htmlonly' comment.
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF714FA033DCB1376922271CBD58A8
A4A36.pygtex) [328 <./images/gc_plot.png>]
(./_minted-Tutorial/80A47C8780CE3021D53829563E81665614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F414FA033DCB1376922271CBD58A8
A4A36.pygtex [329 <./images/dot_plot.png>]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:nuc-dot-plot' on page 330 undefined on input line
 1264.


(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/6D9EA8AD382A3B03E65A62B6462353A114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD14FA033DCB1376922271CBD58A8
A4A36.pygtex [330]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:nuc-dot-plot-scatter' on page 331 undefined on in
put line 1340.


(./_minted-Tutorial/601CCA4B782F1DA528DB81B02480319514FA033DCB1376922271CBD58A8
A4A36.pygtex [331 <./images/dot_plot_scatter.png>])

LaTeX Warning: Reference `fig:paired-end-qual-plot' on page 332 undefined on in
put line 1401.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `chapter:align' on page 332 undefined on input line 14
13.

[332 <./images/SRR001666.png>]

LaTeX Warning: Reference `chapter:align' on page 333 undefined on input line 14
20.


(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC7314FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Reference `sec:consensus' on page 333 undefined on input line 14
31.


LaTeX Warning: Reference `sec:pssm' on page 333 undefined on input line 1432.


LaTeX Warning: Reference `sec:getting_info_content' on page 333 undefined on in
put line 1433.


LaTeX Warning: Reference `sec:sub_matrix' on page 333 undefined on input line 1
434.


LaTeX Warning: Reference `sec:summary_info' on page 333 undefined on input line
 1440.


(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE210C640781732628151051B15D85C
9070A.pygtex [333])
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA481453514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F900C640781732628151051B15D85C
9070A.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1523--1524
[]\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/7F027F6FD8E839F99A1077399D9B8EFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [334]

LaTeX Warning: Reference `sec:summary_info' on page 335 undefined on input line
 1560.


(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB53006514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A4014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D04314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C14FA033DCB1376922271CBD58A8
A4A36.pygtex [335])
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C97367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `sec:align_clustal' on page 336 undefined on input lin
e 1635.


(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C071767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [336])
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C3767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B4940791567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/000D4DEB94FD9E29F9808AD61CE02B1E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1696--1697
\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/63599FE26E47E2B5739BC250C642AA5067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [337])
(./_minted-Tutorial/618B9F1B5BFA1CE93B03A47D26F6F6E367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 338 undefined on input line 17
41.

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

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD06216EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D046EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D90736EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)

LaTeX Warning: Reference `sec:doctest' on page 339 undefined on input line 55.


(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D6EA57A5CF4D3F0EFF6188E720E8
9664B.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
[339]
(./_minted-Tutorial/68D5F2D4CFDBBFF65405364F54DA0BCC0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex [340])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A714FA033DCB1376922271CBD58A8
A4A36.pygtex) [341]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706E14FA033DCB1376922271CBD58A8
A4A36.pygtex [342])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F46EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)

LaTeX Warning: Reference `sec:doctest' on page 343 undefined on input line 282.



(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA2914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B829771114FA033DCB1376922271CBD58A8
A4A36.pygtex [343])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex) [344]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B034566EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC436EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)) [345] (./Tutorial/chapter_advanced.tex
Chapter 22.

LaTeX Warning: Reference `sec:substitution_matrices' on page 346 undefined on i
nput line 36.


Overfull \hbox (61.48412pt too wide) in paragraph at lines 42--44
[]\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 SeqMat []\OT1/cmr/m/n/10 class de-ri
ves from a dic-tio-nary. The dic-tio-nary is of the form [][]\OT1/cmtt/m/n/10 {
(i1,j1):n1, (i1,j2):n2,...,(ik,jk):nk}
[346]
(./_minted-Tutorial/B9AA829C45C3718734961EED663138A314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C91962005319864FA8A80F7CE461D6C614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/949D631F5CFAE16DADE8A9B46DC246FE14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D57E65C15B8337B55081A0ABDE216E8B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/30813B956DA3EC8A9CBD746D69F32D000C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/758DB025D865DFC37AEBF0F3FB3EAF8D0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/0C3F6A07854D0D0ACBB80A71C6F047250C640781732628151051B15D85C
9070A.pygtex) [347]
(./_minted-Tutorial/01598304B617194419D3D22E288DDBB414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2EE2B4E009A2AA257D683D54D33A379814FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Reference `sec:freq_table' on page 348 undefined on input line 1
62.


(./_minted-Tutorial/092222FC5487DB13D5744BF56515DC5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3FBCEA7E512BCF1A100675C665984F1E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F90C13646B17B56314C7FA6500465F7F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (30.74179pt too wide) in paragraph at lines 196--197
[][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the
 log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor

(./_minted-Tutorial/4C4AB8D87E6E7015C3AF4CC8FB7D06D214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/73F214546259C26F0E69498480C6F5E414FA033DCB1376922271CBD58A8
A4A36.pygtex [348])
(./_minted-Tutorial/3C40FC62A59A2301A420D8E25D52D8FB0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/9AD3043016CF73EB0A57C6DFA985DB280C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/D009E3834E447E34C2A0FF5922F938B814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/4E08040CCAE3D812784651E566C1B38314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/ACABC0B74314C452E389E9078BF83C3D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [349] (./Tutorial/chapter_contributing.tex
Chapter 23.

LaTeX Warning: Reference `chapter:cookbook' on page 350 undefined on input line
 32.

[350]
(./_minted-Tutorial/7713FA97EA16E9508BA3E6B9449449256EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A366EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)

LaTeX Warning: Reference `chapter:testing' on page 351 undefined on input line 
85.


LaTeX Warning: Reference `chapter:testing' on page 351 undefined on input line 
101.

[351]) [352] (./Tutorial/chapter_appendix.tex
Chapter 24.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D3267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A46285914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B4214FA033DCB1376922271CBD58A8
A4A36.pygtex [353])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C4214FA033DCB1376922271CBD58A8
A4A36.pygtex)

LaTeX Warning: Reference `sec:SeqIO_compressed' on page 354 undefined on input 
line 91.


(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A20367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [354] [355] [356] [357] (./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_advanced.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 2022/dev/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 (358 pages, 2465376 bytes).
Transcript written on Tutorial.log.
pdflatex --shell-escape "\def\bpversion{1.79}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2021-06-01> patch level 1
L3 programming layer <2021-08-27> (./Tutorial.tex
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2021/02/12 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/generic/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.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/tools/calc.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/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.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/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_advanced.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))
(/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))
(./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.tocpdfTeX warning (ext4): destin
ation with the same identifier (name{page.1}) has been already used, duplicate 
ignored
<to be read again> 
                   \relax 
l.39 ...tions and locations}{29}{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-pyg-prefix.pygstyle)
(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/5B3FAD3A26A9987B2E21C41A827DC1CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [11 <./images/biopython_logo_old.jpg>]
Overfull \hbox (2.99303pt too wide) in paragraph at lines 188--190
\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.

(./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [14])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [15]
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE070C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B021334678185567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [16])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [17]) [18] (./Tutorial/chapter_seq_objects.tex
Chapter 3.

(./_minted-Tutorial/674F0422DD30F7C4B4E808093732659367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/55B4E33A5EF0F1A0B51702F25755DA0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [19]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/533611943FA3AA7E144BE9661F0999DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/99F306D6A0BEAEBD98D7199579E70E7A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E9762250467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [20])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D938642067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C27067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/06A7ACEFB26AA7DD59C8205B22EBC3D967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [21])
(./_minted-Tutorial/8FDF9BC99C1716A778F3C36AB623FB7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D39467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [22])
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF1767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C875367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [23])
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B38667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [24])
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF8267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD6467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF9867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/183C1BBBB8FD6ED15EF6C8F03298A19767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B5599067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [25]
(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [26])
(./_minted-Tutorial/06DBC59F2EAD33E7A95188853787661567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [27]
(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C33867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE45167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [28])
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8009655B8BB14028E5E1BDE9BD4B27E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1107FF2DF5C0B4B87F12506011FBD20867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [29])
(./_minted-Tutorial/6BB61362276E8D90F0EB6BF36B274A6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [30] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

(./_minted-Tutorial/B805770413E9199C6B5EFC63A944737F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [31]
(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D40767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [32])
(./_minted-Tutorial/510764EE0BB38AD6C688E719896775070C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D84982267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD208567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D90C640781732628151051B15D85C
9070A.pygtex [33])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA60167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [34])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F92667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [35] [36]
(./_minted-Tutorial/2D75ABBC1FC42B7382049A62E37C0E4D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [37])
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/269F8765456CC9B88BDF6A41BC90473E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5B76E9A877CC1A76394FE84519866D4467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [38])
(./_minted-Tutorial/18A924CDEFC2ADA66753F94C892F56B167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F9C8B11D1FC2422B35CE8DD6A855273967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B4967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C7567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/86F990EF8173435624D9A400AC90995967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [39])
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E392067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [40])
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F968967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B234067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [41])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [42])
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A8567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/186CFAEA86C7F6492ED0972D7BC46FE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D245767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF8267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [43]
(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF171850166967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [44])
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [45]
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B879367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [46] (./Tutorial/chapter_seqio.tex
Chapter 5.

(./_minted-Tutorial/DBAB0A8061EF77EEA47B4AA55BAA583C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB67814FA033DCB1376922271CBD58A8
A4A36.pygtex [47])
(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE50095414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F114FA033DCB1376922271CBD58A8
A4A36.pygtex [48])
(./_minted-Tutorial/C82398A4A04383A063D2E6488112305214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC049107360C640781732628151051B15D85C
9070A.pygtex) [49]
(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C260C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD16222114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD8214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [50])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E7345114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC3950C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE070C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/693D94A81EEABF91A72754E60DEB360614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/AD214E544DAF411AB89A7DCBECDEFFD10C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/E5529B4EE3E3DFEBAAC551606BEAEC6114FA033DCB1376922271CBD58A8
A4A36.pygtex [51])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C9167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [52])
(./_minted-Tutorial/AFDE811EFDEDCFD9BBD0CAA9BF7F35C267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C0967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [53]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD47614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E42159900C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D714FA033DCB1376922271CBD58A8
A4A36.pygtex [54])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA60C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/3A5DDBC5C437B752848EE8AB449D41AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [55])
(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [56])
(./_minted-Tutorial/A1A806B513EE80294615F1F6C56CA22F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/1075DB6AF9E4A3F207521105E503858714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB814FA033DCB1376922271CBD58A8
A4A36.pygtex [57])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E830C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/53F70E2F1CBA6BCBDCE4071375628CF767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [58]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C7867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF406567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A36467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6209F8400B12665DC9E51BC20774DF7014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [59])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 851--856
\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/D52DA4EEEEE2BF0FBE89EE253714929D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (4.48064pt too wide) in paragraph at lines 894--897
[]\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/D41A88D88AB398F0C3B719A5C7D017C16EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex [60])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E4106EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A277767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [61]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C647167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [62]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD734214FA033DCB1376922271CBD58A8
A4A36.pygtex [63])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C60C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D40C640781732628151051B15D85C
9070A.pygtex [64])
(./_minted-Tutorial/C194E2231D844AE7D0223173D2A8999114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/67EFA0AEA2A7C63922644A13FBF91A3767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [65]
(./_minted-Tutorial/F1D514FF0D281415CACA329B41D1275667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/218C0A230BCAE3B7E030880B471BA86367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AA1E8DC650125C8460BF37E380CAC1AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1435F1CEA90A4D217A423340747F87F067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CA5B97CA60402CA0078F215AFF31799567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA14FA033DCB1376922271CBD58A8
A4A36.pygtex [66])
(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F5314FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1341--1343
\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(...)

(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [67]
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1385--1389
[]\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/D3AF6542680CA390CDA8C8DF87C693D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D749A84299CF58E876E9A899069830DB14FA033DCB1376922271CBD58A8
A4A36.pygtex)) [68] (./Tutorial/chapter_align.tex
Chapter 6.

(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF420C640781732628151051B15D85C
9070A.pygtex [69])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [70])
(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A3107767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F20C640781732628151051B15D85C
9070A.pygtex) [71]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C56040767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD3310C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B445330C640781732628151051B15D85C
9070A.pygtex [72])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF75667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE0C640781732628151051B15D85C
9070A.pygtex) [73]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A140C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF0200C640781732628151051B15D85C
9070A.pygtex [74])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C50C640781732628151051B15D85C
9070A.pygtex) [75]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D31867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A237144770C640781732628151051B15D85C
9070A.pygtex [76])
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/9776F24C4F96F850E549BEF997E4D18C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F402467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F0C640781732628151051B15D85C
9070A.pygtex [77])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF1890C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF990C640781732628151051B15D85C
9070A.pygtex [78])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F1614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F560C640781732628151051B15D85C
9070A.pygtex [79])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2590B11C695B984E246A0A91734F786C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [80]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [81])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B7169267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB0067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E5967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [82])
(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A925367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34725A02F7895E565E5A29E2AC23E8B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E139611EBF30A11F71B774B00CB422D667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [83]
(./_minted-Tutorial/1FE6956CA319233DB7A5C00C9BEC6D4367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/523928538FA511A925EC995B1803BD1667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [84]
(./_minted-Tutorial/7D984F47D0B3A0329DBE2A791B527F5367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E89367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C6306467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [85])
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A44267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F98636867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [86])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B04567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/544A0904C171F7ACED98D10D90A2BBA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1128--1132
[]\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/008DB28D2F01F3F29F1F82EB0591003367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AE24E0D965703AA4106AE5CF699F0A9A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [87])
(./_minted-Tutorial/801A8AB951B5DA791C92C02EB6139DB567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/80957FF2744A858A2D626820D87665F167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [88])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E745467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C4AEB9BD8A76F10ACD8C01403E911E8C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/512DFE88FFA610D4550AF5A23966733167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [89]
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A24067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [90]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC72660C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/798933B773DD1AAF5C2DC54E06491DCF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/44B6EBA222E5AE2CF0E223148840D8AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF38567467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4988824A3CF97A3309EED328C1CB00D167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [91])
(./_minted-Tutorial/DF151703751D72BD556402B910190A8767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA8867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) [92]
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3B28841A01F9F481844677E14CA7D2A367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2203C1F3E2BE8BEF505556D02F8F382C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F209167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [93])
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [94])
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (0.78606pt too wide) in paragraph at lines 1686--1689
\OT1/cmr/m/n/10 The new [][]\OT1/cmtt/m/n/10 Bio.Align.PairwiseAligner []\OT1/c
mr/m/n/10 im-ple-ments the Needleman-Wunsch, Smith-Waterman, Go-toh (three-

(./_minted-Tutorial/554024580088332FAF0EA9296BACE82E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E36167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0ED9274F8C36E3C47BA70FD5BADC364467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [95])
(./_minted-Tutorial/A6265A24C74E31AABCC4CBCDC431287F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71831DAF6DA69540332844566CA78C5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E5E00F47BD7A0C8BC5F881852628386867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [96])
(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE0467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0EDAB1611DCCA854E910FF7DD9D639FA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [97])
(./_minted-Tutorial/F08297D25DBB0EC458EEDF5510780E9567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3DC3D3FA19AFC359663B271CAF187B4867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/17CE58BCB76575958EE7A76C89836E6967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [98])
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1903--1907
[]\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 1903--1907
[]\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

Overfull \hbox (32.852pt too wide) in paragraph at lines 1972--2016
[][]
[99]
(./_minted-Tutorial/52E7DD48238DDBFB9DE1318A616EEA0467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE191167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [100] [101])
(./_minted-Tutorial/9EAAC9128F41783D91F19053824A0E3267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB867167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8AC2E9641A86FDB767AE88F57311BBC267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [102])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9680AE27F087032C33AE5BA458DF8E9C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D0167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6C96493DCAF9B522114CF4E5E2ED59EF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [103]
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A3429659267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5F255D6E493419E5F523F2A975278067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E2D8402A42C488B43E823D056683EE7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C93EE09C24214EFB103597E967BC093E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AD99642E498E0D36D353C8D0E91819C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [104])
(./_minted-Tutorial/147547C6C0B329E642CE7584B58DDCED67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0F1FEB8757C2ABBEFF5A5933C033854A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C2A81981348FC122290D4BF339EF28067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [105])
(./_minted-Tutorial/0D2A1E880F29600B639B45481855F3CF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F1B1BD63B0E1791A94C1591A879316E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E0CC5559A1B54F1DFFC0C95E9F657BC967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C3A68CFDB89C0C63A10B21CD7364FEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [106]
(./_minted-Tutorial/6A00D4BA65DCCBE19BE0A5C25F13423067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [107]
(./_minted-Tutorial/7808362E1897955C4D84B6A5C725B37067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/082EF6E387B649F7F6B9332ECA3C14FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C8E736723204677A93FE4D75F2EB836567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E1F81118C07022DC3AE1F5936BE043AA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57D2FD508C41C176AD7A00FFAD0280C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3363B2217CB2D6762D6F05CF96CEB6EB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [108]
(./_minted-Tutorial/6AFB7518828CB5CE2786BB1F05FA196667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A2CB6704BA931CF6F3C30DE5475D088D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [109])
(./_minted-Tutorial/F4D1EFD0A75F8F251D61853DB5B12A7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94D69571A69F80E3CCD32B0AFD10CBB467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E624B311569CC6FAA91D2E8671D827FB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [110])
(./_minted-Tutorial/7442AA52B0FC887EC2AAC73A4E59FFFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA7767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [111])
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF79660067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2671--2672
\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/F89522EF58FB067C6521C367C713471667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE2067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71A68A4BDF8B5654D3E2E0470AE163B467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CE4E999FF33F9D09A2BB895447AA462967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [112]
(./_minted-Tutorial/3E4691AEB06522E457CDE497E3092DE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2E1DF2678D7C68CA2C465BCE6BBBBD6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C149B172A838F697839B85AE70CC6CDB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [113])
(./_minted-Tutorial/467CA50C36874E405E988587FEC0768667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/819EB88A2CBCC7948E4BEBE7FB9F80EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22DC4F8C7ADBE16392AA93A6EF2819D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/171A69BE62E368AD65396E23A20B1DEE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A1C712272F319372A1AB78DEB403D23367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [114])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A7367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [115])
(./_minted-Tutorial/F31773576B5C3B14C8BCFC3D71E2671467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [116])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E656D3A6BB3675CEC995C2C398DA729367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31A4214F0316300852C263796C130BE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [117])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AB42E81B0039139237BF82BA22516C8B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F45B7CF5E8DCF44722DA12A77C5BD96967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/256D8F4D1BB7E6301923B808B6EEB34567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7AFBDEDDA8F411FC4281444B70E6021E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [118])
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE313567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9730D42326723F9A4A3771D68D644E7C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E3A6838E914945B67D684750F42B90B267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [119])
(./_minted-Tutorial/A117079E905A3317941FA3CB9457C22567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA82527867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F68009367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [120])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/54D7EA4835796C5C4162263077D6191C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D8624166470767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B50C640781732628151051B15D85C
9070A.pygtex [121])
(./_minted-Tutorial/BCCC189D6984A3CAE23757DF96064B4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DFB937A17182FF8FB5EABF3F70A58B0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D0C640781732628151051B15D85C
9070A.pygtex [122])
(./_minted-Tutorial/4DC21B98C2C48E89E7C16C6BAB13C5CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9ED67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A29DE03FF59071EADD7632CC7B11243E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [123])
(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5D9F7C1083DA643BDA1083E79D82EF2067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/20711981BAB695B8006B7A92E4859CF667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [124] (./Tutorial/chapter_blast.tex
Chapter 7.
[125]
(./_minted-Tutorial/04BEBF413314D7A51FC0F91D3066CE4F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [126])
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C20467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/B402706802BF02F25F9B09CDB22A3FEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [127]) [128]
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C20467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE521800467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F4039467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDFE599DAB8ED6AC4F17D4FC6F0230BC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [129])
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D23867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F90D3141F79DD2447A9059C65E1C6B4367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B19240C640781732628151051B15D85C
9070A.pygtex [130]) Excluding 'htmlonly' comment.
Excluding 'htmlonly' comment.

LaTeX Warning: Float too large for page by 32.27644pt on input line 478.

) [131] [132 <./images/BlastRecord.png>] [133 <./images/PSIBlastRecord.png>]
(./Tutorial/chapter_searchio.tex
Chapter 8.

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C
9070A.pygtex) [134]
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/0EF47CD31A1F702FF10BD5C95E6D18FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [135])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B5195567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [136])
(./_minted-Tutorial/5218313E7181C19A936D3F4347E1930A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7BE69614D007F3BE3249A547A9661D0767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE32767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [137])
(./_minted-Tutorial/DC6D0E585B2AACAC1C88A760863B4E4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/130BC5013C07805E69A888444A0B34DB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [138]
(./_minted-Tutorial/0E8B9F4E4323CB258CA049D41E4AB7F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAA6FD197F3F78FDFB781210387FEC2667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [139])
(./_minted-Tutorial/67A62206561049F4B7E307FD79F028C967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5E1CC554EC31697163DDD9D33E32A45667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [140])
(./_minted-Tutorial/0A806FC81D8F7F64321B4A6911027F0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [141]
(./_minted-Tutorial/DC76D831C6E940E11ED2C9452F770E0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A61EC24A4603554A3865574A6B7378067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [142]
(./_minted-Tutorial/4D85AB21D9819B066A1C948098FDB54B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE57357767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4D9A79F8BB08FCA20BAEA3DFAAA08BA467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/62792AA2C0390B83FD6A91F3B267312A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [143])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD88044467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C78767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (27.24287pt too wide) in paragraph at lines 738--740
[]\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/338C616C7128C3DB7FFD516F5C2BDA1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [144])
(./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [145])
(./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [146]
(./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B41343A9090DC4C41F9EC69AB6DEDE1B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [147]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054
\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/B5F76D201899B345CB64AACD67C7346067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085
[]\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/0AB25750C7D89E832295045C60D6B8C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [148])
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E986867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E4B312798560C8CE4ABF272A364D9E2F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/35C0940CA4025285AAECA54EF82C993367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1160--1163
[]\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/BDE985FA3ADA6B0D37013C3D5F37C17667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [149] [150] (./Tutorial/chapter_entrez.tex
Chapter 9.
[151]
(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [152]
(./_minted-Tutorial/7692669934D8ED6DEE1B8B668474542167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [153])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C00867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FAC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [154])
(./_minted-Tutorial/1FE33E4DDF6E596EA7687FB6F017F09967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C6867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A4BD3C61B53064F601B4477CDD3106A667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [155])
(./_minted-Tutorial/36931D2CFB3ECF0D53B3D7376832300467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/ED23259F6CF56D8483B68EF02BB7325067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [156]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F314767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [157] [158])
(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D514FA033DCB1376922271CBD58A8
A4A36.pygtex [159])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F48767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF00867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [160])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5AB8B67C801B8858B19590FE5D018BA367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [161])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC3867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E096EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/0290A0C926605EF68EF2EEEAEB078A0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [162])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF380C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E710C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB860C640781732628151051B15D85C
9070A.pygtex) [163]
(./_minted-Tutorial/BE0AC194CA3417BFC49309A9791ED35B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B0C640781732628151051B15D85C
9070A.pygtex [164])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [165]
(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/97FFA15DF713393C0351F9F947AC446667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34883991B974FF1C1BE2D18B230693C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [166])
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/079D37C5A2B3943F37FA4CC9C5C43BC767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5056BF2116652C732E1D8E3CDA11D6AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [167]
(./_minted-Tutorial/4997CC17B3360B104654D2ED20FA8B4067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A126667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F20190C640781732628151051B15D85C
9070A.pygtex [168])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B62467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9C337E8D92F5A543D90F4D2C8BCBF18367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [169])
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B875C8F385654DD9607A0DAA82B3371067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [170])
(./_minted-Tutorial/F62235DAC4152853E8C6EBBD7E2D286167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [171]
(./_minted-Tutorial/491F8A9C8CFC3BB4763B296852A6D1D567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F7725E37E412C564C008C3BCECB547CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B64203867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [172])
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8F151290BCF14625BA5E4CD26A7FB1E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [173])
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A7279767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB384867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4EDDF5C23B0FCCC279960365B499A16C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [174])
(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C4567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB9364967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [175]
(./_minted-Tutorial/FE862EFCF9F786EA3C4D97E3821A5CAA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E2467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F963367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D57414FA033DCB1376922271CBD58A8
A4A36.pygtex [176])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA14FA033DCB1376922271CBD58A8
A4A36.pygtex [177])
(./_minted-Tutorial/826A4111F6CE74D7A673B6C8F5681FC367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F52B50369F8EBC15506CCA30EE3F873367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [178] (./Tutorial/chapter_uniprot.tex
Chapter 10.

(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A8667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A66867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD676867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/930B60BD569CAAF368B0E614553F303067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [179]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA651918267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/68D834E8AB9E722FD7953C65DB7E9FDB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD6922867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D1467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [180])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A451791867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF256282240C640781732628151051B15D85C
9070A.pygtex [181])
(./_minted-Tutorial/3876A0F1CD2CBCD824C73B244059EE4767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [182])
(./_minted-Tutorial/7A92C6B39F0BC9AE063090BDDCD011DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B0C640781732628151051B15D85C
9070A.pygtex [183])
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC78367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [184]
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3C3B5BB472E9A4A7B3F5BFA41CA60C7867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (24.29903pt too wide) in paragraph at lines 362--363
[]\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/483E7285F7FA2A76D28505EE0DE792D467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [185])
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 405--406
[]\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/DF2DA17EFC0F6336210C74066809B75367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9457A436D281E066D350873A88476E5967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [186])
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A80C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AB8625F199818648FAC2C5737C2D032067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [187])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E8616967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [188] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C2285367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E6908567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [189])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA738867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB3567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36B58FEFA589A67048E7D5B63D489DAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB823167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [190]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E1867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D17667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A02467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [191])
(./_minted-Tutorial/05F3B09A7CBE08B1C91DE55284F12C2867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [192]
Overfull \hbox (13.022pt too wide) in paragraph at lines 263--265
\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)
Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D97967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [193] [194 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD85567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB24767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E272762267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [195]
(./_minted-Tutorial/2F13678C6026DEBF0D98D4214CDF499867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DE3953D86837855582C4B8B9F38D7FD667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [196]
(./_minted-Tutorial/D15D1F955440960DB3C5206BF3EEE29E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/652F2E49D1B3634A04F3CB950B38570467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [197])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC8809867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB1249267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/84495A3B19FA62DBFC292B309E5DE1E567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [198])
(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [199]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB9067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B12867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [200])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF23189967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/87466E9C05D4662C6164A2AFA3A69C4967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC266367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA3967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [201])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E66767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/200193443B83EEADE7971FACFD86F16D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A49EF93DADD431750435FD5125A74A0567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [202])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D51872E4871C96F9D4DDBFAF9C4DF2EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [203]
Overfull \hbox (42.26714pt too wide) in paragraph at lines 953--957
\OT1/cmr/m/n/10 breaks and dis-or-dered residues and atoms as de-scribed above 
are han-dled cor-rectly. \OT1/cmtt/m/n/10 structure[]rebuild[]test(entity)

Overfull \hbox (3.8904pt too wide) in paragraph at lines 973--993
[][] 

(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [204])

LaTeX Warning: Command \r invalid in math mode on input line 1046.


(./_minted-Tutorial/0F60C02FB1C0A5EBADB8EF693216594667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [205]
(./_minted-Tutorial/163F04F633C696E8F41EBFFBB74DAF9D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/84DC73903FA70E943C63131089E2ED9F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [206] [207]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB1567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [208]
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [209]) [210] (./Tutorial/chapter_popgen.tex
Chapter 12.

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B115204AFF525DDD4F3CF69B79C0739114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC14FA033DCB1376922271CBD58A8
A4A36.pygtex [211])) [212] (./Tutorial/chapter_phylo.tex
Chapter 13.

(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC56710C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE1586EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C2467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [213])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3E6F23F473B4E07E8F7181EEE5B0B4A567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [214]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178
[]\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/29624A9666C9430AABADF395148BBF2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [215 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/6382EC6908438B3E67C757E70A11466C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [216 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/6D2EF2116C7B06D5B8D357EA567F832E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A145A6C1AAD034F2FF71DE52310A2BD467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/787FD2B6485DC30362A59A325340738367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F5567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [217])
(./_minted-Tutorial/9DD9A1F0A4FFCEEE15CCB35AFAE0B5FB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7692F6F4FEC56E165A881DE3F8A965167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) Excluding 'htmlonly' comment. [218]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445
\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"})
[219 <./images/phylo-draw-example.png>]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496
[]\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
 ,
[220]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF614FA033DCB1376922271CBD58A8
A4A36.pygtex) [221]
(./_minted-Tutorial/5B477DBF8C94B1E6FDC020E6A741C0DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A317CBB9F004B52870B25AB07ACF279167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (4.04672pt too wide) in paragraph at lines 708--711
[]\OT1/cmr/m/n/10 A sim-i-lar wrap-per for RAxML ([][]$\OT1/cmtt/m/n/10 https :
 / / sco . h-[]its . org / exelixis / software . html$[][]\OT1/cmr/m/n/10 ) was
 added in Biopy-
[222]
(./_minted-Tutorial/4A4A0B08C37495B73842BFCD67A687D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [223]) [224] (./Tutorial/chapter_motifs.tex
Chapter 14.

(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F155F8EF3B63ECD9B6708A42B8F5F72A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [225])
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE7567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D17767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D25717367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/666DFB2D351C7C4DE86ECB38CCBB491867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [226])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F6124319202267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB247667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [227]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA0C640781732628151051B15D85C
9070A.pygtex [228])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [229])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D140C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C7667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF920C640781732628151051B15D85C
9070A.pygtex [230])
(./_minted-Tutorial/B5E175DBFE536E62D3BB466A47FD029F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [231])
(./_minted-Tutorial/7F5E0E05D69E7F9EC30F2A5CD5D9B5F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [232])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/696A69FC8317D40C8605CBADFDA5D87767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [233]
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6382581C9B01D86887B13EFD1FA7AFA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C37867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C1EF8469C0F4B427273EE106072F9E6667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [234])
(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F80C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E440C640781732628151051B15D85C
9070A.pygtex [235])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 602--605
\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/147DE2DA7F37C2A5A1C1344033AB8B8467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [236])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E01205367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA70C640781732628151051B15D85C
9070A.pygtex [237])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8C09EEE739CAD078852B77A784E1269267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

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


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


(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [238] [239])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F2640667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF5149567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE7060567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [240])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [241])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B3F030F5FA6A7817CFA605062601C81267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E22567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E4867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [242])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8F2A64376DB87D5A7AB48BFE3760B0B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [243])
(./_minted-Tutorial/22387CA0FB9349FBC21B30A09B80342067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A8167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA16167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [244]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E2567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A509267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C8607367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE97067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [245])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [246])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E32267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD726160367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA247367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [247])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA1667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [248]
(./_minted-Tutorial/63EC9F933A4699B71D633AB9C35237C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5032B21DEC5EBE299D472B0AF220432A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A2667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F44720C640781732628151051B15D85C
9070A.pygtex) [249]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [250]) [251] (./Tutorial/chapter_cluster.tex
Chapter 15.
[252] [253] [254] [255]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED414067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2CEA2595B9B8CEAD10513E8D15566D0167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE60173582767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A250014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [256])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 244--245
\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/05DC01C08B8EDF71F86E3C3A9C28EB3467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [257] [258]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [259]
(./_minted-Tutorial/C286E2777B917B774560CBDC7CF9262667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8
A4A36.pygtex) [260] [261]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 422--423
[][]\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/015798D317E9D8732518AFD186C997CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C23904926786173967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [262]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE2267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [263]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F7267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF889505567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [264])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8
A4A36.pygtex) [265]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C17567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [266]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 653--655
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [267]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A7DB1B14B8C3B59B03D102D4BEECDD167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D220C09E8614EBE54BD07A8C18AAC3367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [268]
Overfull \hbox (25.39864pt too wide) in paragraph at lines 737--748
 [] 
[269]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [270]
(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [271]
(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA850467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [272]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 927--929
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [273])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF5867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 984--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 
. 
[274] (./Tutorial/chapter_learning.tex
Chapter 16.
[275]
(./_minted-Tutorial/8C8664D7942C9DDA1DE175A432DAD57267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [276])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D87A6F5674B92E17575B5F1479772CA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [277]) [278]
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB09667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D40267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94C0A9A9293B19D950018F966B967E8167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [279])
(./_minted-Tutorial/A1B56761C52CC91D59E84159B69EC85E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 280.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 280.

[280]

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 288.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 288.


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 300.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 300.


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA59567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FF01A8BA64DD59AF7C1265FFBD6C1B5267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/27D68FCC443982B3438F0C03A4D541D667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [281])
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC1567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/10829292EF1E211AEAC19B179A46CD1067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7F43A5B55F7492DFDBA4E17BF7F34F4767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [282])) [283] (./Tutorial/chapter_graphics.tex
Chapter 17.
[284]
(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D81614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B03514FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA714FA033DCB1376922271CBD58A8
A4A36.pygtex [285]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E14FA033DCB1376922271CBD58A8
A4A36.pygtex [286 <./images/plasmid_linear.png (PNG copy)>]) [287 <./images/pla
smid_circular.png (PNG copy)>]
(./_minted-Tutorial/5D58687CD77437A3DD50DABD32F1536714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/0EA68B85D005018D196EB15C866B9F3814FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D85014FA033DCB1376922271CBD58A8
A4A36.pygtex [288]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B9414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C14FA033DCB1376922271CBD58A8
A4A36.pygtex [289] [290 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB14FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A14FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/0ABDE2E70066A4661C3DDA814AC7225814FA033DCB1376922271CBD58A8
A4A36.pygtex [291] [292 <./images/GD_sigils.png>] [293 <./images/GD_sigil_arrow
_shafts.png>] [294 <./images/GD_sigil_arrow_heads.png>] [295])
Excluding 'htmlonly' comment. [296 <./images/plasmid_linear_nice.png (PNG copy)
>] [297 <./images/plasmid_circular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA8914FA033DCB1376922271CBD58A8
A4A36.pygtex [298])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177A14FA033DCB1376922271CBD58A8
A4A36.pygtex [299]) Excluding 'htmlonly' comment. [300 <./images/three_track_si
mple.png>]
(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA11114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB14FA033DCB1376922271CBD58A8
A4A36.pygtex [301])
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD184014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C2814FA033DCB1376922271CBD58A8
A4A36.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. [302] Excluding 'htmlonly' comment. [303 <./image
s/three_track_cl.png>] [304 <./images/three_track_cl2a.png>]
(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F72841497714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F14FA033DCB1376922271CBD58A8
A4A36.pygtex) [305]
(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C14FA033DCB1376922271CBD58A8
A4A36.pygtex [306] [307 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A7514FA033DCB1376922271CBD58A8
A4A36.pygtex [308]) Excluding 'htmlonly' comment.) [309]
(./Tutorial/chapter_kegg.tex
Chapter 18.

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [310]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B14FA033DCB1376922271CBD58A8
A4A36.pygtex [311])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C950C640781732628151051B15D85C
9070A.pygtex)) [312] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [313]
(./_minted-Tutorial/F7E0F1384D5EE10CDFEDB2428F50CCC667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB4467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB08167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B6CD5F177651EF61E679B9FAF6C25BE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [314])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D720667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [315])
(./_minted-Tutorial/EE7361AC934053D42AE642DBF97DE34A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [316])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [317] (./Tutorial/chapter_cookbook.tex
Chapter 20.

(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB14FA033DCB1376922271CBD58A8
A4A36.pygtex [318])
(./_minted-Tutorial/FF8B764D5420CEF9ECE1CDD6385A3BDC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E5716467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [319]
(./_minted-Tutorial/D24532DF36691735DACEF9DD7062845467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/54D3F8BEB8094C8ADFFB26585CE1463814FA033DCB1376922271CBD58A8
A4A36.pygtex [320])
(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F6414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A023964706114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B14FA033DCB1376922271CBD58A8
A4A36.pygtex) [321]
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC6554114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE40879314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D914FA033DCB1376922271CBD58A8
A4A36.pygtex [322])
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA214FA033DCB1376922271CBD58A8
A4A36.pygtex) [323]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF64183114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F3545014FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (5.83499pt too wide) in paragraph at lines 452--456
\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/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (4.57849pt too wide) in paragraph at lines 473--475
\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 . 
[324]
(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA55614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A14FA033DCB1376922271CBD58A8
A4A36.pygtex [325])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F891514FA033DCB1376922271CBD58A8
A4A36.pygtex [326]) [327]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C3114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC4073736714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/8ADDD83BA2CAFB21C875C8B9C0986B9B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B514FA033DCB1376922271CBD58A8
A4A36.pygtex [328])
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [329]
(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/41250203CD471B54840A6F5E1188318D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [330]
(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BAE95C3681F5665B01248E86DAC866B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B214FA033DCB1376922271CBD58A8
A4A36.pygtex [331])
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A630520C640781732628151051B15D85C
9070A.pygtex [332])
(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B714FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment. [333]
Overfull \hbox (4.00363pt too wide) in paragraph at lines 1114--1117
[]\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/7C23BDB073E316E7093E4D3A77BD752E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD14FA033DCB1376922271CBD58A8
A4A36.pygtex [334 <./images/hist_plot.png>]) Excluding 'htmlonly' comment.
Excluding 'htmlonly' comment.
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF714FA033DCB1376922271CBD58A8
A4A36.pygtex) [335 <./images/gc_plot.png>]
(./_minted-Tutorial/80A47C8780CE3021D53829563E81665614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F414FA033DCB1376922271CBD58A8
A4A36.pygtex [336 <./images/dot_plot.png>]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/6D9EA8AD382A3B03E65A62B6462353A114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD14FA033DCB1376922271CBD58A8
A4A36.pygtex [337]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/601CCA4B782F1DA528DB81B02480319514FA033DCB1376922271CBD58A8
A4A36.pygtex [338 <./images/dot_plot_scatter.png>])
Excluding 'htmlonly' comment. [339 <./images/SRR001666.png>]
(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC7314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE210C640781732628151051B15D85C
9070A.pygtex [340])
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA481453514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F900C640781732628151051B15D85C
9070A.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1523--1524
[]\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/7F027F6FD8E839F99A1077399D9B8EFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [341]
(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB53006514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A4014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D04314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C14FA033DCB1376922271CBD58A8
A4A36.pygtex [342])
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C97367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C071767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [343])
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C3767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B4940791567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/000D4DEB94FD9E29F9808AD61CE02B1E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1696--1697
\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/63599FE26E47E2B5739BC250C642AA5067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [344])
(./_minted-Tutorial/618B9F1B5BFA1CE93B03A47D26F6F6E367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [345] (./Tutorial/chapter_testing.tex
Chapter 21.

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD06216EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D046EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D90736EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D6EA57A5CF4D3F0EFF6188E720E8
9664B.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
[346]
(./_minted-Tutorial/68D5F2D4CFDBBFF65405364F54DA0BCC0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex [347])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A714FA033DCB1376922271CBD58A8
A4A36.pygtex) [348]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706E14FA033DCB1376922271CBD58A8
A4A36.pygtex [349])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F46EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA2914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B829771114FA033DCB1376922271CBD58A8
A4A36.pygtex [350])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex) [351]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B034566EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC436EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)) [352] (./Tutorial/chapter_advanced.tex
Chapter 22.

Overfull \hbox (61.48412pt too wide) in paragraph at lines 42--44
[]\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 SeqMat []\OT1/cmr/m/n/10 class de-ri
ves from a dic-tio-nary. The dic-tio-nary is of the form [][]\OT1/cmtt/m/n/10 {
(i1,j1):n1, (i1,j2):n2,...,(ik,jk):nk}
[353]
(./_minted-Tutorial/B9AA829C45C3718734961EED663138A314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C91962005319864FA8A80F7CE461D6C614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/949D631F5CFAE16DADE8A9B46DC246FE14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D57E65C15B8337B55081A0ABDE216E8B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/30813B956DA3EC8A9CBD746D69F32D000C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/758DB025D865DFC37AEBF0F3FB3EAF8D0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/0C3F6A07854D0D0ACBB80A71C6F047250C640781732628151051B15D85C
9070A.pygtex) [354]
(./_minted-Tutorial/01598304B617194419D3D22E288DDBB414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2EE2B4E009A2AA257D683D54D33A379814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/092222FC5487DB13D5744BF56515DC5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3FBCEA7E512BCF1A100675C665984F1E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F90C13646B17B56314C7FA6500465F7F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (30.74179pt too wide) in paragraph at lines 196--197
[][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the
 log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor

(./_minted-Tutorial/4C4AB8D87E6E7015C3AF4CC8FB7D06D214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/73F214546259C26F0E69498480C6F5E414FA033DCB1376922271CBD58A8
A4A36.pygtex [355])
(./_minted-Tutorial/3C40FC62A59A2301A420D8E25D52D8FB0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/9AD3043016CF73EB0A57C6DFA985DB280C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/D009E3834E447E34C2A0FF5922F938B814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/4E08040CCAE3D812784651E566C1B38314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/ACABC0B74314C452E389E9078BF83C3D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [356] (./Tutorial/chapter_contributing.tex
Chapter 23.
[357]
(./_minted-Tutorial/7713FA97EA16E9508BA3E6B9449449256EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A366EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex) [358]) [359] (./Tutorial/chapter_appendix.tex
Chapter 24.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D3267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A46285914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B4214FA033DCB1376922271CBD58A8
A4A36.pygtex [360])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C4214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A20367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [361] [362] [363] [364] (./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_advanced.aux)
(./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux))

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 (365 pages, 2524645 bytes).
Transcript written on Tutorial.log.
pdflatex --shell-escape "\def\bpversion{1.79}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2021-06-01> patch level 1
L3 programming layer <2021-08-27> (./Tutorial.tex
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2021/02/12 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/generic/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.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/tools/calc.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/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.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/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_advanced.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))
(/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))
(./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.tocpdfTeX warning (ext4): destin
ation with the same identifier (name{page.1}) has been already used, duplicate 
ignored
<to be read again> 
                   \relax 
l.39 ...tions and locations}{36}{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-pyg-prefix.pygstyle)
(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/5B3FAD3A26A9987B2E21C41A827DC1CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [11 <./images/biopython_logo_old.jpg>]
Overfull \hbox (2.99303pt too wide) in paragraph at lines 188--190
\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.

(./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [14])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [15]
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE070C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B021334678185567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [16])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [17]) [18] (./Tutorial/chapter_seq_objects.tex
Chapter 3.

(./_minted-Tutorial/674F0422DD30F7C4B4E808093732659367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/55B4E33A5EF0F1A0B51702F25755DA0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [19]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/533611943FA3AA7E144BE9661F0999DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/99F306D6A0BEAEBD98D7199579E70E7A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E9762250467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [20])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D938642067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C27067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/06A7ACEFB26AA7DD59C8205B22EBC3D967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [21])
(./_minted-Tutorial/8FDF9BC99C1716A778F3C36AB623FB7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D39467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [22])
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF1767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C875367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [23])
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B38667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [24])
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF8267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD6467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF9867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/183C1BBBB8FD6ED15EF6C8F03298A19767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B5599067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [25]
(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [26])
(./_minted-Tutorial/06DBC59F2EAD33E7A95188853787661567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [27]
(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C33867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE45167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [28])
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8009655B8BB14028E5E1BDE9BD4B27E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1107FF2DF5C0B4B87F12506011FBD20867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [29])
(./_minted-Tutorial/6BB61362276E8D90F0EB6BF36B274A6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [30] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

(./_minted-Tutorial/B805770413E9199C6B5EFC63A944737F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [31]
(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D40767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [32])
(./_minted-Tutorial/510764EE0BB38AD6C688E719896775070C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D84982267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD208567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D90C640781732628151051B15D85C
9070A.pygtex [33])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4A0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA60167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [34])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F92667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [35] [36]
(./_minted-Tutorial/2D75ABBC1FC42B7382049A62E37C0E4D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [37])
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/269F8765456CC9B88BDF6A41BC90473E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5B76E9A877CC1A76394FE84519866D4467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [38])
(./_minted-Tutorial/18A924CDEFC2ADA66753F94C892F56B167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F9C8B11D1FC2422B35CE8DD6A855273967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B4967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C7567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/86F990EF8173435624D9A400AC90995967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [39])
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E392067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [40])
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F968967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B234067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [41])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [42])
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A8567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/186CFAEA86C7F6492ED0972D7BC46FE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D245767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF8267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [43]
(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF171850166967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [44])
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [45]
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B879367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [46] (./Tutorial/chapter_seqio.tex
Chapter 5.

(./_minted-Tutorial/DBAB0A8061EF77EEA47B4AA55BAA583C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB67814FA033DCB1376922271CBD58A8
A4A36.pygtex [47])
(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE50095414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F114FA033DCB1376922271CBD58A8
A4A36.pygtex [48])
(./_minted-Tutorial/C82398A4A04383A063D2E6488112305214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AED14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC049107360C640781732628151051B15D85C
9070A.pygtex) [49]
(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C260C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD16222114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD8214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [50])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E7345114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2A14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC3950C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE070C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/693D94A81EEABF91A72754E60DEB360614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/AD214E544DAF411AB89A7DCBECDEFFD10C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/E5529B4EE3E3DFEBAAC551606BEAEC6114FA033DCB1376922271CBD58A8
A4A36.pygtex [51])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C9167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [52])
(./_minted-Tutorial/AFDE811EFDEDCFD9BBD0CAA9BF7F35C267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C0967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [53]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD47614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E42159900C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D714FA033DCB1376922271CBD58A8
A4A36.pygtex [54])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05D0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA60C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/3A5DDBC5C437B752848EE8AB449D41AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [55])
(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [56])
(./_minted-Tutorial/A1A806B513EE80294615F1F6C56CA22F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528F0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/1075DB6AF9E4A3F207521105E503858714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB814FA033DCB1376922271CBD58A8
A4A36.pygtex [57])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E830C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/53F70E2F1CBA6BCBDCE4071375628CF767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [58]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C7867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF406567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A36467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6209F8400B12665DC9E51BC20774DF7014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [59])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 851--856
\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/D52DA4EEEEE2BF0FBE89EE253714929D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (4.48064pt too wide) in paragraph at lines 894--897
[]\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/D41A88D88AB398F0C3B719A5C7D017C16EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex [60])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E4106EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A277767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [61]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C647167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [62]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD734214FA033DCB1376922271CBD58A8
A4A36.pygtex [63])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C60C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D40C640781732628151051B15D85C
9070A.pygtex [64])
(./_minted-Tutorial/C194E2231D844AE7D0223173D2A8999114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/67EFA0AEA2A7C63922644A13FBF91A3767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [65]
(./_minted-Tutorial/F1D514FF0D281415CACA329B41D1275667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/218C0A230BCAE3B7E030880B471BA86367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AA1E8DC650125C8460BF37E380CAC1AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1435F1CEA90A4D217A423340747F87F067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CA5B97CA60402CA0078F215AFF31799567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EA14FA033DCB1376922271CBD58A8
A4A36.pygtex [66])
(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F5314FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1341--1343
\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(...)

(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [67]
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1385--1389
[]\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/D3AF6542680CA390CDA8C8DF87C693D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D749A84299CF58E876E9A899069830DB14FA033DCB1376922271CBD58A8
A4A36.pygtex)) [68] (./Tutorial/chapter_align.tex
Chapter 6.

(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF420C640781732628151051B15D85C
9070A.pygtex [69])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [70])
(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A3107767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F20C640781732628151051B15D85C
9070A.pygtex) [71]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C56040767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD3310C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B445330C640781732628151051B15D85C
9070A.pygtex [72])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF75667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DE0C640781732628151051B15D85C
9070A.pygtex) [73]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A140C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF0200C640781732628151051B15D85C
9070A.pygtex [74])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C50C640781732628151051B15D85C
9070A.pygtex) [75]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D31867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A237144770C640781732628151051B15D85C
9070A.pygtex [76])
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/9776F24C4F96F850E549BEF997E4D18C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F402467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479F0C640781732628151051B15D85C
9070A.pygtex [77])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF1890C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF990C640781732628151051B15D85C
9070A.pygtex [78])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F1614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F560C640781732628151051B15D85C
9070A.pygtex [79])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2590B11C695B984E246A0A91734F786C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [80]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [81])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B7169267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB0067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E5967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [82])
(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A925367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34725A02F7895E565E5A29E2AC23E8B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E139611EBF30A11F71B774B00CB422D667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [83]
(./_minted-Tutorial/1FE6956CA319233DB7A5C00C9BEC6D4367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/523928538FA511A925EC995B1803BD1667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [84]
(./_minted-Tutorial/7D984F47D0B3A0329DBE2A791B527F5367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E89367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C6306467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [85])
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A44267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F98636867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [86])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B04567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/544A0904C171F7ACED98D10D90A2BBA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1128--1132
[]\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/008DB28D2F01F3F29F1F82EB0591003367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AE24E0D965703AA4106AE5CF699F0A9A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [87])
(./_minted-Tutorial/801A8AB951B5DA791C92C02EB6139DB567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/80957FF2744A858A2D626820D87665F167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [88])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E745467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C4AEB9BD8A76F10ACD8C01403E911E8C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/512DFE88FFA610D4550AF5A23966733167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [89]
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A24067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [90]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC72660C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/798933B773DD1AAF5C2DC54E06491DCF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/44B6EBA222E5AE2CF0E223148840D8AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF38567467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4988824A3CF97A3309EED328C1CB00D167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [91])
(./_minted-Tutorial/DF151703751D72BD556402B910190A8767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA8867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd) [92]
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3B28841A01F9F481844677E14CA7D2A367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2203C1F3E2BE8BEF505556D02F8F382C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F209167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [93])
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [94])
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (0.78606pt too wide) in paragraph at lines 1686--1689
\OT1/cmr/m/n/10 The new [][]\OT1/cmtt/m/n/10 Bio.Align.PairwiseAligner []\OT1/c
mr/m/n/10 im-ple-ments the Needleman-Wunsch, Smith-Waterman, Go-toh (three-

(./_minted-Tutorial/554024580088332FAF0EA9296BACE82E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E36167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0ED9274F8C36E3C47BA70FD5BADC364467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [95])
(./_minted-Tutorial/A6265A24C74E31AABCC4CBCDC431287F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71831DAF6DA69540332844566CA78C5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E5E00F47BD7A0C8BC5F881852628386867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [96])
(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE0467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0EDAB1611DCCA854E910FF7DD9D639FA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [97])
(./_minted-Tutorial/F08297D25DBB0EC458EEDF5510780E9567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3DC3D3FA19AFC359663B271CAF187B4867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/17CE58BCB76575958EE7A76C89836E6967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [98])
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1903--1907
[]\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 1903--1907
[]\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

Overfull \hbox (32.852pt too wide) in paragraph at lines 1972--2016
[][]
[99]
(./_minted-Tutorial/52E7DD48238DDBFB9DE1318A616EEA0467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE191167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [100] [101])
(./_minted-Tutorial/9EAAC9128F41783D91F19053824A0E3267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB867167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8AC2E9641A86FDB767AE88F57311BBC267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [102])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9680AE27F087032C33AE5BA458DF8E9C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D0167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6C96493DCAF9B522114CF4E5E2ED59EF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [103]
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A3429659267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5F255D6E493419E5F523F2A975278067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E2D8402A42C488B43E823D056683EE7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C93EE09C24214EFB103597E967BC093E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AD99642E498E0D36D353C8D0E91819C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [104])
(./_minted-Tutorial/147547C6C0B329E642CE7584B58DDCED67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0F1FEB8757C2ABBEFF5A5933C033854A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C2A81981348FC122290D4BF339EF28067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [105])
(./_minted-Tutorial/0D2A1E880F29600B639B45481855F3CF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F1B1BD63B0E1791A94C1591A879316E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E0CC5559A1B54F1DFFC0C95E9F657BC967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C3A68CFDB89C0C63A10B21CD7364FEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [106]
(./_minted-Tutorial/6A00D4BA65DCCBE19BE0A5C25F13423067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [107]
(./_minted-Tutorial/7808362E1897955C4D84B6A5C725B37067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/082EF6E387B649F7F6B9332ECA3C14FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C8E736723204677A93FE4D75F2EB836567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E1F81118C07022DC3AE1F5936BE043AA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57D2FD508C41C176AD7A00FFAD0280C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3363B2217CB2D6762D6F05CF96CEB6EB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [108]
(./_minted-Tutorial/6AFB7518828CB5CE2786BB1F05FA196667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A2CB6704BA931CF6F3C30DE5475D088D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [109])
(./_minted-Tutorial/F4D1EFD0A75F8F251D61853DB5B12A7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94D69571A69F80E3CCD32B0AFD10CBB467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E624B311569CC6FAA91D2E8671D827FB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [110])
(./_minted-Tutorial/7442AA52B0FC887EC2AAC73A4E59FFFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA7767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [111])
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF79660067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2671--2672
\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/F89522EF58FB067C6521C367C713471667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE2067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71A68A4BDF8B5654D3E2E0470AE163B467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CE4E999FF33F9D09A2BB895447AA462967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [112]
(./_minted-Tutorial/3E4691AEB06522E457CDE497E3092DE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2E1DF2678D7C68CA2C465BCE6BBBBD6367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C149B172A838F697839B85AE70CC6CDB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [113])
(./_minted-Tutorial/467CA50C36874E405E988587FEC0768667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/819EB88A2CBCC7948E4BEBE7FB9F80EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22DC4F8C7ADBE16392AA93A6EF2819D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/171A69BE62E368AD65396E23A20B1DEE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A1C712272F319372A1AB78DEB403D23367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [114])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A7367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [115])
(./_minted-Tutorial/F31773576B5C3B14C8BCFC3D71E2671467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [116])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E656D3A6BB3675CEC995C2C398DA729367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31A4214F0316300852C263796C130BE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [117])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AB42E81B0039139237BF82BA22516C8B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F45B7CF5E8DCF44722DA12A77C5BD96967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/256D8F4D1BB7E6301923B808B6EEB34567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7AFBDEDDA8F411FC4281444B70E6021E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [118])
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE313567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9730D42326723F9A4A3771D68D644E7C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E3A6838E914945B67D684750F42B90B267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [119])
(./_minted-Tutorial/A117079E905A3317941FA3CB9457C22567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA82527867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F68009367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [120])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/54D7EA4835796C5C4162263077D6191C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D8624166470767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B50C640781732628151051B15D85C
9070A.pygtex [121])
(./_minted-Tutorial/BCCC189D6984A3CAE23757DF96064B4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DFB937A17182FF8FB5EABF3F70A58B0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555D0C640781732628151051B15D85C
9070A.pygtex [122])
(./_minted-Tutorial/4DC21B98C2C48E89E7C16C6BAB13C5CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9ED67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A29DE03FF59071EADD7632CC7B11243E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [123])
(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5D9F7C1083DA643BDA1083E79D82EF2067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/20711981BAB695B8006B7A92E4859CF667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [124] (./Tutorial/chapter_blast.tex
Chapter 7.
[125]
(./_minted-Tutorial/04BEBF413314D7A51FC0F91D3066CE4F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [126])
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C20467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/B402706802BF02F25F9B09CDB22A3FEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [127]) [128]
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD0867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C20467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE521800467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F4039467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDFE599DAB8ED6AC4F17D4FC6F0230BC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [129])
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D23867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F90D3141F79DD2447A9059C65E1C6B4367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B19240C640781732628151051B15D85C
9070A.pygtex [130]) Excluding 'htmlonly' comment.
Excluding 'htmlonly' comment.

LaTeX Warning: Float too large for page by 32.27644pt on input line 478.

) [131] [132 <./images/BlastRecord.png>] [133 <./images/PSIBlastRecord.png>]
(./Tutorial/chapter_searchio.tex
Chapter 8.

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346E0C640781732628151051B15D85C
9070A.pygtex) [134]
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/0EF47CD31A1F702FF10BD5C95E6D18FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [135])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B5195567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [136])
(./_minted-Tutorial/5218313E7181C19A936D3F4347E1930A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7BE69614D007F3BE3249A547A9661D0767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE32767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [137])
(./_minted-Tutorial/DC6D0E585B2AACAC1C88A760863B4E4E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/130BC5013C07805E69A888444A0B34DB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [138]
(./_minted-Tutorial/0E8B9F4E4323CB258CA049D41E4AB7F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAA6FD197F3F78FDFB781210387FEC2667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [139])
(./_minted-Tutorial/67A62206561049F4B7E307FD79F028C967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5E1CC554EC31697163DDD9D33E32A45667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [140])
(./_minted-Tutorial/0A806FC81D8F7F64321B4A6911027F0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [141]
(./_minted-Tutorial/DC76D831C6E940E11ED2C9452F770E0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A61EC24A4603554A3865574A6B7378067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [142]
(./_minted-Tutorial/4D85AB21D9819B066A1C948098FDB54B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE57357767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4D9A79F8BB08FCA20BAEA3DFAAA08BA467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/62792AA2C0390B83FD6A91F3B267312A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [143])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD88044467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C78767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (27.24287pt too wide) in paragraph at lines 738--740
[]\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/338C616C7128C3DB7FFD516F5C2BDA1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/64A5027CB01EBC16D0BBBCFA493BDAE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A353690967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B35C581DC0102E618595FCC0BE2AFE9867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [144])
(./_minted-Tutorial/23A338D38E31EFFAE0C56C5A5AAB567A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F1953B67CE735DCB6EDDECF134C333B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69130C6EA441D4D1DEB35E75101C9AB967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [145])
(./_minted-Tutorial/688EDDC69F177DE7868A4B0C32B1499267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E295C926B8D61E45F6C5FA1C0767BFD467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [146]
(./_minted-Tutorial/4CFB05EC7DD8FA77EFE275E81B5A1B9767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B41343A9090DC4C41F9EC69AB6DEDE1B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [147]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1050--1054
\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/B5F76D201899B345CB64AACD67C7346067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (20.13245pt too wide) in paragraph at lines 1080--1085
[]\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/0AB25750C7D89E832295045C60D6B8C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [148])
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E986867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E4B312798560C8CE4ABF272A364D9E2F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/35C0940CA4025285AAECA54EF82C993367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1160--1163
[]\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/BDE985FA3ADA6B0D37013C3D5F37C17667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [149] [150] (./Tutorial/chapter_entrez.tex
Chapter 9.
[151]
(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [152]
(./_minted-Tutorial/7692669934D8ED6DEE1B8B668474542167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA3667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [153])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C00867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FAC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [154])
(./_minted-Tutorial/1FE33E4DDF6E596EA7687FB6F017F09967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C6867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A4BD3C61B53064F601B4477CDD3106A667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [155])
(./_minted-Tutorial/36931D2CFB3ECF0D53B3D7376832300467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/ED23259F6CF56D8483B68EF02BB7325067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [156]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F314767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [157] [158])
(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D514FA033DCB1376922271CBD58A8
A4A36.pygtex [159])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F48767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF00867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [160])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5AB8B67C801B8858B19590FE5D018BA367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [161])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC3867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E096EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/0290A0C926605EF68EF2EEEAEB078A0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [162])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF380C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E710C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB860C640781732628151051B15D85C
9070A.pygtex) [163]
(./_minted-Tutorial/BE0AC194CA3417BFC49309A9791ED35B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24D0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1B0C640781732628151051B15D85C
9070A.pygtex [164])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [165]
(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AAD0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/97FFA15DF713393C0351F9F947AC446667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34883991B974FF1C1BE2D18B230693C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [166])
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/079D37C5A2B3943F37FA4CC9C5C43BC767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5056BF2116652C732E1D8E3CDA11D6AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [167]
(./_minted-Tutorial/4997CC17B3360B104654D2ED20FA8B4067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A126667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F20190C640781732628151051B15D85C
9070A.pygtex [168])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B62467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7A14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9C337E8D92F5A543D90F4D2C8BCBF18367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [169])
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B875C8F385654DD9607A0DAA82B3371067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [170])
(./_minted-Tutorial/F62235DAC4152853E8C6EBBD7E2D286167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [171]
(./_minted-Tutorial/491F8A9C8CFC3BB4763B296852A6D1D567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F7725E37E412C564C008C3BCECB547CD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B64203867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [172])
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8F151290BCF14625BA5E4CD26A7FB1E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [173])
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A7279767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB384867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4EDDF5C23B0FCCC279960365B499A16C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [174])
(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C4567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB9364967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [175]
(./_minted-Tutorial/FE862EFCF9F786EA3C4D97E3821A5CAA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E2467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F963367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D57414FA033DCB1376922271CBD58A8
A4A36.pygtex [176])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFA14FA033DCB1376922271CBD58A8
A4A36.pygtex [177])
(./_minted-Tutorial/826A4111F6CE74D7A673B6C8F5681FC367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F52B50369F8EBC15506CCA30EE3F873367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [178] (./Tutorial/chapter_uniprot.tex
Chapter 10.

(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A8667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A66867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD676867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/930B60BD569CAAF368B0E614553F303067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [179]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA651918267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/68D834E8AB9E722FD7953C65DB7E9FDB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD6922867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D1467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C0667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [180])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A451791867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09AB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF256282240C640781732628151051B15D85C
9070A.pygtex [181])
(./_minted-Tutorial/3876A0F1CD2CBCD824C73B244059EE4767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AA0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [182])
(./_minted-Tutorial/7A92C6B39F0BC9AE063090BDDCD011DF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5B0C640781732628151051B15D85C
9070A.pygtex [183])
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC78367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [184]
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3C3B5BB472E9A4A7B3F5BFA41CA60C7867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (24.29903pt too wide) in paragraph at lines 362--363
[]\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/483E7285F7FA2A76D28505EE0DE792D467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [185])
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 405--406
[]\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/DF2DA17EFC0F6336210C74066809B75367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9457A436D281E066D350873A88476E5967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [186])
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A80C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AB8625F199818648FAC2C5737C2D032067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [187])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E8616967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [188] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C2285367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E6908567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [189])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA738867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB3567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36B58FEFA589A67048E7D5B63D489DAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB823167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [190]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E1867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D17667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A02467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [191])
(./_minted-Tutorial/05F3B09A7CBE08B1C91DE55284F12C2867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECEC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [192]
Overfull \hbox (13.022pt too wide) in paragraph at lines 263--265
\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)
Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D97967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [193] [194 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD85567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB24767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E272762267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A1267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [195]
(./_minted-Tutorial/2F13678C6026DEBF0D98D4214CDF499867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DE3953D86837855582C4B8B9F38D7FD667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [196]
(./_minted-Tutorial/D15D1F955440960DB3C5206BF3EEE29E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/652F2E49D1B3634A04F3CB950B38570467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [197])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC8809867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB1249267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/84495A3B19FA62DBFC292B309E5DE1E567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [198])
(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [199]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB9067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B12867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [200])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF23189967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/87466E9C05D4662C6164A2AFA3A69C4967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC266367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA3967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [201])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E66767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/200193443B83EEADE7971FACFD86F16D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A49EF93DADD431750435FD5125A74A0567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [202])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D51872E4871C96F9D4DDBFAF9C4DF2EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [203]
Overfull \hbox (42.26714pt too wide) in paragraph at lines 953--957
\OT1/cmr/m/n/10 breaks and dis-or-dered residues and atoms as de-scribed above 
are han-dled cor-rectly. \OT1/cmtt/m/n/10 structure[]rebuild[]test(entity)

Overfull \hbox (3.8904pt too wide) in paragraph at lines 973--993
[][] 

(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [204])

LaTeX Warning: Command \r invalid in math mode on input line 1046.


(./_minted-Tutorial/0F60C02FB1C0A5EBADB8EF693216594667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [205]
(./_minted-Tutorial/163F04F633C696E8F41EBFFBB74DAF9D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/84DC73903FA70E943C63131089E2ED9F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [206] [207]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB1567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [208]
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [209]) [210] (./Tutorial/chapter_popgen.tex
Chapter 12.

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B115204AFF525DDD4F3CF69B79C0739114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FC14FA033DCB1376922271CBD58A8
A4A36.pygtex [211])) [212] (./Tutorial/chapter_phylo.tex
Chapter 13.

(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC56710C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE1586EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C2467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [213])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3E6F23F473B4E07E8F7181EEE5B0B4A567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [214]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178
[]\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/29624A9666C9430AABADF395148BBF2767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [215 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/6382EC6908438B3E67C757E70A11466C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [216 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/6D2EF2116C7B06D5B8D357EA567F832E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A145A6C1AAD034F2FF71DE52310A2BD467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/787FD2B6485DC30362A59A325340738367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F5567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [217])
(./_minted-Tutorial/9DD9A1F0A4FFCEEE15CCB35AFAE0B5FB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E7692F6F4FEC56E165A881DE3F8A965167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) Excluding 'htmlonly' comment. [218]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 438--445
\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"})
[219 <./images/phylo-draw-example.png>]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 493--496
[]\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
 ,
[220]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF614FA033DCB1376922271CBD58A8
A4A36.pygtex) [221]
(./_minted-Tutorial/5B477DBF8C94B1E6FDC020E6A741C0DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A317CBB9F004B52870B25AB07ACF279167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (4.04672pt too wide) in paragraph at lines 708--711
[]\OT1/cmr/m/n/10 A sim-i-lar wrap-per for RAxML ([][]$\OT1/cmtt/m/n/10 https :
 / / sco . h-[]its . org / exelixis / software . html$[][]\OT1/cmr/m/n/10 ) was
 added in Biopy-
[222]
(./_minted-Tutorial/4A4A0B08C37495B73842BFCD67A687D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [223]) [224] (./Tutorial/chapter_motifs.tex
Chapter 14.

(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F155F8EF3B63ECD9B6708A42B8F5F72A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D0367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [225])
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE7567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989C67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D17767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D25717367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/666DFB2D351C7C4DE86ECB38CCBB491867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [226])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F6124319202267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB247667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [227]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FA0C640781732628151051B15D85C
9070A.pygtex [228])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [229])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D140C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C7667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF920C640781732628151051B15D85C
9070A.pygtex [230])
(./_minted-Tutorial/B5E175DBFE536E62D3BB466A47FD029F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [231])
(./_minted-Tutorial/7F5E0E05D69E7F9EC30F2A5CD5D9B5F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [232])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/696A69FC8317D40C8605CBADFDA5D87767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [233]
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6382581C9B01D86887B13EFD1FA7AFA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C37867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C1EF8469C0F4B427273EE106072F9E6667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [234])
(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F80C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6AB0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB00C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E440C640781732628151051B15D85C
9070A.pygtex [235])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909F67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 602--605
\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/147DE2DA7F37C2A5A1C1344033AB8B8467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [236])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E01205367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9E0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA70C640781732628151051B15D85C
9070A.pygtex [237])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8C09EEE739CAD078852B77A784E1269267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

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


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


(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [238] [239])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F2640667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF5149567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE7060567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [240])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C7467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [241])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B3F030F5FA6A7817CFA605062601C81267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E22567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F2167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E4867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [242])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8F2A64376DB87D5A7AB48BFE3760B0B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [243])
(./_minted-Tutorial/22387CA0FB9349FBC21B30A09B80342067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A8167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA16167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [244]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E2567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A509267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C8607367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE97067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [245])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [246])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E32267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD726160367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA247367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [247])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA1667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [248]
(./_minted-Tutorial/63EC9F933A4699B71D633AB9C35237C667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5032B21DEC5EBE299D472B0AF220432A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A2667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F44720C640781732628151051B15D85C
9070A.pygtex) [249]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [250]) [251] (./Tutorial/chapter_cluster.tex
Chapter 15.
[252] [253] [254] [255]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED414067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/2CEA2595B9B8CEAD10513E8D15566D0167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE60173582767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A250014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [256])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 244--245
\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/05DC01C08B8EDF71F86E3C3A9C28EB3467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [257] [258]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [259]
(./_minted-Tutorial/C286E2777B917B774560CBDC7CF9262667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8
A4A36.pygtex) [260] [261]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 422--423
[][]\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/015798D317E9D8732518AFD186C997CA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C23904926786173967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [262]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203AD67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE2267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [263]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F7267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D4167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF889505567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [264])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED1814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7AC14FA033DCB1376922271CBD58A8
A4A36.pygtex) [265]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C17567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [266]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 653--655
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [267]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABAB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/6A7DB1B14B8C3B59B03D102D4BEECDD167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7D220C09E8614EBE54BD07A8C18AAC3367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [268]
Overfull \hbox (25.39864pt too wide) in paragraph at lines 737--748
 [] 
[269]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [270]
(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [271]
(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA850467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [272]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 927--929
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D7067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [273])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF5867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 984--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 
. 
[274] (./Tutorial/chapter_learning.tex
Chapter 16.
[275]
(./_minted-Tutorial/8C8664D7942C9DDA1DE175A432DAD57267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [276])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D87A6F5674B92E17575B5F1479772CA967B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [277]) [278]
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB09667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CE67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D40267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/94C0A9A9293B19D950018F966B967E8167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [279])
(./_minted-Tutorial/A1B56761C52CC91D59E84159B69EC85E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 280.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 280.

[280]

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 288.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 288.


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)

Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 300.


Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref)                removing `math shift' on input line 300.


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA59567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FF01A8BA64DD59AF7C1265FFBD6C1B5267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/27D68FCC443982B3438F0C03A4D541D667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [281])
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC1567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/10829292EF1E211AEAC19B179A46CD1067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7F43A5B55F7492DFDBA4E17BF7F34F4767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [282])) [283] (./Tutorial/chapter_graphics.tex
Chapter 17.
[284]
(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D81614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B03514FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA714FA033DCB1376922271CBD58A8
A4A36.pygtex [285]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36E14FA033DCB1376922271CBD58A8
A4A36.pygtex [286 <./images/plasmid_linear.png (PNG copy)>]) [287 <./images/pla
smid_circular.png (PNG copy)>]
(./_minted-Tutorial/5D58687CD77437A3DD50DABD32F1536714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/0EA68B85D005018D196EB15C866B9F3814FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D85014FA033DCB1376922271CBD58A8
A4A36.pygtex [288]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B9414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80C14FA033DCB1376922271CBD58A8
A4A36.pygtex [289] [290 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEB14FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863A14FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/0ABDE2E70066A4661C3DDA814AC7225814FA033DCB1376922271CBD58A8
A4A36.pygtex [291] [292 <./images/GD_sigils.png>] [293 <./images/GD_sigil_arrow
_shafts.png>] [294 <./images/GD_sigil_arrow_heads.png>] [295])
Excluding 'htmlonly' comment. [296 <./images/plasmid_linear_nice.png (PNG copy)
>] [297 <./images/plasmid_circular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA8914FA033DCB1376922271CBD58A8
A4A36.pygtex [298])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177A14FA033DCB1376922271CBD58A8
A4A36.pygtex [299]) Excluding 'htmlonly' comment. [300 <./images/three_track_si
mple.png>]
(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA11114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFB14FA033DCB1376922271CBD58A8
A4A36.pygtex [301])
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD184014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C2814FA033DCB1376922271CBD58A8
A4A36.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. [302] Excluding 'htmlonly' comment. [303 <./image
s/three_track_cl.png>] [304 <./images/three_track_cl2a.png>]
(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F72841497714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FE14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAF14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67F14FA033DCB1376922271CBD58A8
A4A36.pygtex) [305]
(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192C14FA033DCB1376922271CBD58A8
A4A36.pygtex [306] [307 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A7514FA033DCB1376922271CBD58A8
A4A36.pygtex [308]) Excluding 'htmlonly' comment.) [309]
(./Tutorial/chapter_kegg.tex
Chapter 18.

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C7167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [310]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4B14FA033DCB1376922271CBD58A8
A4A36.pygtex [311])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C950C640781732628151051B15D85C
9070A.pygtex)) [312] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [313]
(./_minted-Tutorial/F7E0F1384D5EE10CDFEDB2428F50CCC667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB4467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB08167B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/B6CD5F177651EF61E679B9FAF6C25BE867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [314])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D720667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [315])
(./_minted-Tutorial/EE7361AC934053D42AE642DBF97DE34A67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [316])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E667B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [317] (./Tutorial/chapter_cookbook.tex
Chapter 20.

(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EB14FA033DCB1376922271CBD58A8
A4A36.pygtex [318])
(./_minted-Tutorial/FF8B764D5420CEF9ECE1CDD6385A3BDC14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E5716467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [319]
(./_minted-Tutorial/D24532DF36691735DACEF9DD7062845467B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/54D3F8BEB8094C8ADFFB26585CE1463814FA033DCB1376922271CBD58A8
A4A36.pygtex [320])
(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F6414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A023964706114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03B14FA033DCB1376922271CBD58A8
A4A36.pygtex) [321]
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC6554114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE40879314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D914FA033DCB1376922271CBD58A8
A4A36.pygtex [322])
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA214FA033DCB1376922271CBD58A8
A4A36.pygtex) [323]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF64183114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F3545014FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (5.83499pt too wide) in paragraph at lines 452--456
\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/AB16E58608A2F17CC79E69295572088714FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (4.57849pt too wide) in paragraph at lines 473--475
\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 . 
[324]
(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBD14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA55614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64A14FA033DCB1376922271CBD58A8
A4A36.pygtex [325])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9C14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F891514FA033DCB1376922271CBD58A8
A4A36.pygtex [326]) [327]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C3114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC4073736714FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/8ADDD83BA2CAFB21C875C8B9C0986B9B67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B514FA033DCB1376922271CBD58A8
A4A36.pygtex [328])
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CAB14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [329]
(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB8067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEB67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/41250203CD471B54840A6F5E1188318D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [330]
(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/BAE95C3681F5665B01248E86DAC866B867B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B214FA033DCB1376922271CBD58A8
A4A36.pygtex [331])
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A630520C640781732628151051B15D85C
9070A.pygtex [332])
(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CC67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B714FA033DCB1376922271CBD58A8
A4A36.pygtex) Excluding 'htmlonly' comment. [333]
Overfull \hbox (4.00363pt too wide) in paragraph at lines 1114--1117
[]\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/7C23BDB073E316E7093E4D3A77BD752E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CD14FA033DCB1376922271CBD58A8
A4A36.pygtex [334 <./images/hist_plot.png>]) Excluding 'htmlonly' comment.
Excluding 'htmlonly' comment.
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF714FA033DCB1376922271CBD58A8
A4A36.pygtex) [335 <./images/gc_plot.png>]
(./_minted-Tutorial/80A47C8780CE3021D53829563E81665614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F414FA033DCB1376922271CBD58A8
A4A36.pygtex [336 <./images/dot_plot.png>]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/6D9EA8AD382A3B03E65A62B6462353A114FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20AD14FA033DCB1376922271CBD58A8
A4A36.pygtex [337]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/601CCA4B782F1DA528DB81B02480319514FA033DCB1376922271CBD58A8
A4A36.pygtex [338 <./images/dot_plot_scatter.png>])
Excluding 'htmlonly' comment. [339 <./images/SRR001666.png>]
(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC7314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFA0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE210C640781732628151051B15D85C
9070A.pygtex [340])
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643D14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA481453514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F900C640781732628151051B15D85C
9070A.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1523--1524
[]\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/7F027F6FD8E839F99A1077399D9B8EFF67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex) [341]
(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB53006514FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A4014FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D04314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7C14FA033DCB1376922271CBD58A8
A4A36.pygtex [342])
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C97367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FA67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C071767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [343])
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C3767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B4940791567B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/000D4DEB94FD9E29F9808AD61CE02B1E67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1696--1697
\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/63599FE26E47E2B5739BC250C642AA5067B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex [344])
(./_minted-Tutorial/618B9F1B5BFA1CE93B03A47D26F6F6E367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [345] (./Tutorial/chapter_testing.tex
Chapter 21.

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD06216EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D046EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D90736EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D6EA57A5CF4D3F0EFF6188E720E8
9664B.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
[346]
(./_minted-Tutorial/68D5F2D4CFDBBFF65405364F54DA0BCC0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex [347])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A714FA033DCB1376922271CBD58A8
A4A36.pygtex) [348]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706E14FA033DCB1376922271CBD58A8
A4A36.pygtex [349])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F46EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA2914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B829771114FA033DCB1376922271CBD58A8
A4A36.pygtex [350])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F6EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex) [351]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B034566EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC436EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)) [352] (./Tutorial/chapter_advanced.tex
Chapter 22.

Overfull \hbox (61.48412pt too wide) in paragraph at lines 42--44
[]\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 SeqMat []\OT1/cmr/m/n/10 class de-ri
ves from a dic-tio-nary. The dic-tio-nary is of the form [][]\OT1/cmtt/m/n/10 {
(i1,j1):n1, (i1,j2):n2,...,(ik,jk):nk}
[353]
(./_minted-Tutorial/B9AA829C45C3718734961EED663138A314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/C91962005319864FA8A80F7CE461D6C614FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/949D631F5CFAE16DADE8A9B46DC246FE14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/D57E65C15B8337B55081A0ABDE216E8B14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/30813B956DA3EC8A9CBD746D69F32D000C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/758DB025D865DFC37AEBF0F3FB3EAF8D0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/0C3F6A07854D0D0ACBB80A71C6F047250C640781732628151051B15D85C
9070A.pygtex) [354]
(./_minted-Tutorial/01598304B617194419D3D22E288DDBB414FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/2EE2B4E009A2AA257D683D54D33A379814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/092222FC5487DB13D5744BF56515DC5767B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/3FBCEA7E512BCF1A100675C665984F1E14FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/F90C13646B17B56314C7FA6500465F7F14FA033DCB1376922271CBD58A8
A4A36.pygtex)
Overfull \hbox (30.74179pt too wide) in paragraph at lines 196--197
[][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the
 log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor

(./_minted-Tutorial/4C4AB8D87E6E7015C3AF4CC8FB7D06D214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/73F214546259C26F0E69498480C6F5E414FA033DCB1376922271CBD58A8
A4A36.pygtex [355])
(./_minted-Tutorial/3C40FC62A59A2301A420D8E25D52D8FB0C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/9AD3043016CF73EB0A57C6DFA985DB280C640781732628151051B15D85C
9070A.pygtex)
(./_minted-Tutorial/D009E3834E447E34C2A0FF5922F938B814FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/4E08040CCAE3D812784651E566C1B38314FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/ACABC0B74314C452E389E9078BF83C3D67B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [356] (./Tutorial/chapter_contributing.tex
Chapter 23.
[357]
(./_minted-Tutorial/7713FA97EA16E9508BA3E6B9449449256EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex)
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A366EA57A5CF4D3F0EFF6188E720E8
9664B.pygtex) [358]) [359] (./Tutorial/chapter_appendix.tex
Chapter 24.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D3267B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A46285914FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B4214FA033DCB1376922271CBD58A8
A4A36.pygtex [360])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C4214FA033DCB1376922271CBD58A8
A4A36.pygtex)
(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A20367B6D4EEEA70E83368C1BFCE3E2
2EA7D.pygtex)) [361] [362] [363] [364] (./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_advanced.aux)
(./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux))

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 (365 pages, 2524640 bytes).
Transcript written on Tutorial.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2021-06-01> patch level 1
L3 programming layer <2021-08-27>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2021/02/12 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/generic/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/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.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/babel.def
(/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/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/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/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/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 1350--1358
[]\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/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkd8
a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkl8a.pfb></usr/s
hare/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/f
onts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/courier/ucrro8a.pfb>
Output written on biopdb_faq.pdf (15 pages, 163442 bytes).
Transcript written on biopdb_faq.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2021-06-01> patch level 1
L3 programming layer <2021-08-27>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2021/02/12 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/generic/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/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.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/babel.def
(/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/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/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(./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/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 1350--1358
[]\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/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkd8
a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkl8a.pfb></usr/s
hare/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/f
onts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/courier/ucrro8a.pfb>
Output written on biopdb_faq.pdf (15 pages, 165360 bytes).
Transcript written on biopdb_faq.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2021-06-01> patch level 1
L3 programming layer <2021-08-27>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2021/02/12 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/generic/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/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.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/babel.def
(/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/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/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(./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/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 1350--1358
[]\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/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkd8
a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/bookman/ubkl8a.pfb></usr/s
hare/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/f
onts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/courier/ucrro8a.pfb>
Output written on biopdb_faq.pdf (15 pages, 165360 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 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 3.9 --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:232: set -e; \
                             mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/home; \
                             mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples; \
                             cp -a Doc/Tutorial.tex /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc; \
                             cp -a Doc/Tutorial /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc; \
                             cp -a Doc/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc; \
                             cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build; \
                             cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests; \
                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/home python3.9 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_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_3.9/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
ok
test_EmbossPrimer ... ok
test_Entrez ... 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_3.9/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
ok
test_GenomeDiagram ... Warn: Can't find .pfb for face 'Times-Roman'
ok
test_GraphicsBitmaps ... skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics
Can't setFont(Times-Roman) missing the T1 files?
Originally <class 'TypeError'>: makeT1Font() argument 2 must be str, not None
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 ... ok
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_DSSP ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:252: UserWarning: Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match

  warnings.warn(err)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:252: UserWarning: Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match

  warnings.warn(err)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:252: UserWarning: Invalid mmCIF file use --verbose option to see errors

  warnings.warn(err)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:252: UserWarning: Invalid mmCIF file use --verbose option to see errors

  warnings.warn(err)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:252: UserWarning: Invalid mmCIF file use --verbose option to see errors

  warnings.warn(err)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py:252: UserWarning: Invalid mmCIF file use --verbose option to see errors

  warnings.warn(err)
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_Polypeptide ... ok
test_PDB_SASA ... ok
test_PDB_SMCRA ... 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_QCPSuperimposer ... 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_3.9/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
  warnings.warn(
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn("Non-standard molecule type: %s" % 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_3.9/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/InsdcIO.py:548: 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_SubsMat ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat/__init__.py:126: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
  warnings.warn(
ok
test_SwissProt ... ok
test_TCoffee_tool ... ok
test_TogoWS ... skipping. internet not available
test_TreeConstruction ... ok
test_Tutorial ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Seq.py:2008: BiopythonDeprecationWarning: UnknownSeq(length) is deprecated; please use Seq(None, length) instead.
  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_3.9/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_3.9/build/Bio/Seq.py:2954: 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_3.9/build/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
  warnings.warn(
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/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_psw ... 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.substitution_matrices 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.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.ExPASy.cellosaurus 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.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.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.SubsMat docstring test ... ok
Bio.SubsMat.FreqTable docstring test ... ok
Bio.SubsMat.MatrixInfo 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.chisq 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 512 tests in 996.807 seconds

Skipping any tests requiring internet access
Python version: 3.9.7 (default, Sep 30 2021, 19:20:56) 
[GCC 10.3.0]
Operating system: posix linux
	rm -fr -- /tmp/dh-xdg-rundir-6BsDZmay
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 -d /<<BUILDDIR>>/python-biopython-1.79\+dfsg/debian/tmp
	pybuild --install -i python{version} -p 3.9 --dest-dir /<<BUILDDIR>>/python-biopython-1.79\+dfsg/debian/tmp
I: pybuild base:232: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/tmp 
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
  warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
  warnings.warn(
running install
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'
running build_ext
running install_lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/File.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/LogisticRegression.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/MarkovModel.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/MaxEntropy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NaiveBayes.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Seq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqFeature.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqRecord.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/_utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/bgzf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/kNN.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/pairwise2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Affy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Affy/CelFile.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Affy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Affy/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Affy
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Affy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Affy/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Affy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Affy/__pycache__/CelFile.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Affy/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/AlignInfo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_ClustalOmega.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_Clustalw.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_Dialign.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_MSAProbs.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_Mafft.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_Muscle.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_Prank.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_Probcons.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/_TCoffee.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_Muscle.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_Clustalw.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_ClustalOmega.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_Prank.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_Mafft.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_Dialign.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_Probcons.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_TCoffee.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/Applications/__pycache__/_MSAProbs.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/BENNER22 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/BENNER6 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/BENNER74 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/BLOSUM45 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/BLOSUM50 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/BLOSUM62 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/BLOSUM80 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/BLOSUM90 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/DAYHOFF -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/FENG -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/GENETIC -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/GONNET1992 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/HOXD70 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/JOHNSON -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/JONES -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/LEVIN -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/MCLACHLAN -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/MDM78 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/NUC.4.4 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/PAM250 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/PAM30 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/PAM70 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/RAO -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/RISLER -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/SCHNEIDER -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/STR -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/data/TRANS -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/data
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/substitution_matrices/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/_aligners.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/_aligners.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Align/__pycache__/AlignInfo.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/ClustalIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/EmbossIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/Interfaces.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/MafIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/MauveIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/MsfIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/NexusIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/PhylipIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/StockholmIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/ClustalIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/Interfaces.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/EmbossIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/FastaIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/MafIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/MauveIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/MsfIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/NexusIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/PhylipIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/AlignIO/__pycache__/StockholmIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Alphabet
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Alphabet/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Alphabet
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Application
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Application/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Application
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Application/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Application/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Application/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/Applications.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/NCBIWWW.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/NCBIXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/ParseBlastTable.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/Record.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/__pycache__/Record.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/__pycache__/NCBIXML.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/__pycache__/Applications.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/__pycache__/NCBIWWW.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Blast/__pycache__/ParseBlastTable.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/CAPS
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/CAPS/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/CAPS
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/CAPS/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/CAPS/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/CAPS/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster/cluster.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster/cluster.h -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster/clustermodule.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster/_cluster.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Cluster/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign/chisq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign/codonalignment.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign/codonseq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign/__pycache__/codonseq.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign/__pycache__/codonalignment.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/codonalign/__pycache__/chisq.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Compass
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Compass/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Compass
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Compass/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Compass/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Compass/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data/CodonTable.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data/IUPACData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data/SCOPData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data/__pycache__/CodonTable.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data/__pycache__/IUPACData.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Data/__pycache__/SCOPData.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss/Applications.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss/Primer3.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss/PrimerSearch.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss/__pycache__/Applications.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss/__pycache__/PrimerSearch.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Emboss/__pycache__/Primer3.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/Parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/EMBL_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/GenBank_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/HomoloGene.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/MMDB.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/MMDB.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/MMDB_Features.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Access.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Project.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NCBI_all.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NSE.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/NSE.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/OMSSA.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/PDB_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/PIR_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/PRF_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/SP_General.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/SP_General.mod.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/archivearticle.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/archivecustom-classes.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/archivecustom-models.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/archivecustom-modules.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/articlemeta.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/backmatter.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/chars.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/common.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/default-classes.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/default-mixes.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/display.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/eInfo_020511.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/eLink_090910.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/eLink_101123.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/ePost_020511.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/eSearch_020511.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/eSpell.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/eSummary_041029.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/egquery.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/einfo.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/elink_020122.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/esearch.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/esummary-v1.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/format.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/htmltable.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isoamsa.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isoamsb.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isoamsc.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isoamsn.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isoamso.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isoamsr.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isobox.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isocyr1.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isocyr2.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isodia.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isogrk1.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isogrk2.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isogrk3.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isogrk4.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isolat1.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isolat2.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isomfrk.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isomopf.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isomscr.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isonum.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isopub.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/isotech.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/journalmeta.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/link.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/list.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/math.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/mathml2.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/mathml3-qname1.mod -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/mathml3.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/mathmlsetup.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/mmlalias.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/mmlextra.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/modules.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/notat.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/para.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/phrase.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pmc-1.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_020114.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_080101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_090101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_100101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_100301.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_110101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_120101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_130101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_130501.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_140101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_150101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_180101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_180601.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/pubmed_190101.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/references.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/section.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/taxon.dtd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/DTDs/xmlspecchars.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/DTDs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/XSDs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/XSDs/IPGReportSet.xsd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/XSDs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Entrez/__pycache__/Parser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/Enzyme.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/Prodoc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/Prosite.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/ScanProsite.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/cellosaurus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/__pycache__/Enzyme.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/__pycache__/Prodoc.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/__pycache__/Prosite.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/__pycache__/cellosaurus.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/ExPASy/__pycache__/ScanProsite.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank/Record.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank/Scanner.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank/utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank/__pycache__/utils.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank/__pycache__/Scanner.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/GenBank/__pycache__/Record.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Geo/Record.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Geo/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Geo
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Geo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Geo/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Geo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Geo/__pycache__/Record.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Geo/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/BasicChromosome.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/ColorSpiral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/Comparative.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/DisplayRepresentation.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/Distribution.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/KGML_vis.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_Colors.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_Diagram.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_Feature.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_Graph.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/_Track.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_Diagram.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_LinearDrawer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_AbstractDrawer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_FeatureSet.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_Feature.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_Colors.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_GraphSet.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_Graph.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_CircularDrawer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_Track.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/GenomeDiagram/__pycache__/_CrossLink.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/__pycache__/ColorSpiral.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/__pycache__/Comparative.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/__pycache__/BasicChromosome.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/__pycache__/DisplayRepresentation.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/__pycache__/Distribution.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Graphics/__pycache__/KGML_vis.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/DynamicProgramming.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/MarkovModel.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/Trainer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/Utilities.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/__pycache__/MarkovModel.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/__pycache__/Trainer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/__pycache__/DynamicProgramming.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/HMM/__pycache__/Utilities.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/REST.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Compound
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Compound/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Compound
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Compound/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Compound/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Compound/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Enzyme
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Enzyme/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Enzyme
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Enzyme/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Enzyme/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Enzyme/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Gene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Gene/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Gene
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Gene/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Gene/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Gene/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Map
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Map/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Map
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Map/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/Map/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Map/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML/KGML_parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML/KGML_pathway.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML/__pycache__/KGML_parser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/KGML/__pycache__/KGML_pathway.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/KEGG/__pycache__/REST.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf/DefaultParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf/mmtfio.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf/__pycache__/DefaultParser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmtf/__pycache__/mmtfio.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/AbstractPropertyMap.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Atom.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Chain.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Dice.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Entity.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/FragmentMapper.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/HSExposure.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/MMCIF2Dict.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/MMCIFParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Model.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/NACCESS.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/NeighborSearch.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/PDBExceptions.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/PDBIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/PDBList.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/PDBParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/PICIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/PSEA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Polypeptide.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Residue.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/ResidueDepth.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/SASA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/SCADIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Selection.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Structure.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/StructureAlignment.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/StructureBuilder.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/Superimposer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/ic_data.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/ic_rebuild.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/internal_coords.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/mmcifio.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/parse_pdb_header.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/vectors.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/DSSP.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/QCPSuperimposer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/QCPSuperimposer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/QCPSuperimposer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/QCPSuperimposer
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/QCPSuperimposer/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/QCPSuperimposer/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/QCPSuperimposer/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/kdtrees.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/kdtrees.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/PDBParser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/PDBExceptions.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/StructureBuilder.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Structure.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Entity.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/internal_coords.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Atom.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/vectors.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Polypeptide.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/ic_data.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Model.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Chain.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Residue.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/parse_pdb_header.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/MMCIFParser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/MMCIF2Dict.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/PDBList.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/PDBIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/mmcifio.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Selection.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Superimposer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/StructureAlignment.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/DSSP.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/AbstractPropertyMap.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/ResidueDepth.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/HSExposure.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/FragmentMapper.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/Dice.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/NeighborSearch.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/SASA.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/NACCESS.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/ic_rebuild.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/PICIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/SCADIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PDB/__pycache__/PSEA.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Medline
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Medline/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Medline
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Medline/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Medline/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Medline/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/alignace.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/clusterbuster.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/mast.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/matrix.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/meme.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/minimal.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/pfm.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/thresholds.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/transfac.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/xms.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/applications/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/applications/_xxmotif.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/applications
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/applications/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/applications/__pycache__/_xxmotif.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/applications/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/jaspar
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/jaspar
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar/db.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/jaspar
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/jaspar/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/jaspar/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/jaspar/__pycache__/db.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/jaspar/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/_pwm.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/_pwm.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/matrix.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/meme.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/transfac.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/thresholds.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/alignace.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/clusterbuster.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/pfm.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/xms.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/mast.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/motifs/__pycache__/minimal.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/Nexus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/Nodes.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/StandardData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/Trees.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/cnexus.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/cnexus.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/__pycache__/Nexus.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/__pycache__/StandardData.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/__pycache__/Trees.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Nexus/__pycache__/Nodes.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR/NOEtools.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR/xpktools.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR/__pycache__/xpktools.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/NMR/__pycache__/NOEtools.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep/Graph.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep/MultiGraph.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep/__pycache__/MultiGraph.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/Rep/__pycache__/Graph.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Pathway/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype/phen_micro.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype/pm_fitting.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype/__pycache__/phen_micro.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/phenotype/__pycache__/pm_fitting.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/Controller.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/EasyController.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/FileParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/LargeFileParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/__pycache__/FileParser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/__pycache__/Controller.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/__pycache__/EasyController.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/GenePop/__pycache__/LargeFileParser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/PopGen/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction/PrintFormat.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction/Restriction.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction/Restriction_Dictionary.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction/__pycache__/Restriction.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction/__pycache__/Restriction_Dictionary.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Restriction/__pycache__/PrintFormat.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/Cla.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/Des.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/Dom.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/Hie.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/Raf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/Residues.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/__pycache__/Des.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/__pycache__/Cla.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/__pycache__/Residues.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/__pycache__/Hie.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/__pycache__/Dom.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SCOP/__pycache__/Raf.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlatIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy/NCBIStandalone.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy/ParserSupport.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy/__pycache__/NCBIStandalone.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_legacy/__pycache__/ParserSupport.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/_base.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/hit.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/hsp.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/query.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/__pycache__/query.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/__pycache__/_base.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/__pycache__/hit.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/_model/__pycache__/hsp.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO/blast_tab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO/blast_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO/blast_xml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO/__pycache__/blast_tab.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO/__pycache__/blast_xml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/BlastIO/__pycache__/blast_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HHsuiteIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HHsuiteIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HHsuiteIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HHsuiteIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HHsuiteIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HHsuiteIO/__pycache__/hhsuite2_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HHsuiteIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/_base.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/__pycache__/hmmer2_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/__pycache__/_base.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/__pycache__/hmmer3_domtab.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/__pycache__/hmmer3_tab.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/HmmerIO/__pycache__/hmmer3_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/_base.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/__pycache__/exonerate_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/__pycache__/_base.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/__pycache__/exonerate_vulgar.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/ExonerateIO/__pycache__/exonerate_cigar.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/InterproscanIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/InterproscanIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/InterproscanIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/InterproscanIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/InterproscanIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/InterproscanIO/__pycache__/interproscan_xml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/InterproscanIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/__pycache__/_utils.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/__pycache__/_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/__pycache__/BlatIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SearchIO/__pycache__/FastaIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/AbiIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/AceIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/GckIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/IgIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/InsdcIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/Interfaces.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/NibIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/PdbIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/PhdIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/PirIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/QualityIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/SeqXmlIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/SffIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/SnapGeneIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/SwissIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/TabIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/TwoBitIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/UniprotIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/XdnaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/_twoBitIO.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/_twoBitIO.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/AbiIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/Interfaces.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/AceIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/FastaIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/GckIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/IgIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/InsdcIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/NibIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/PdbIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/PhdIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/QualityIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/PirIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/SeqXmlIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/SffIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/SnapGeneIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/SwissIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/TabIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/TwoBitIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/UniprotIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/XdnaIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqIO/__pycache__/_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/CheckSum.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/CodonUsage.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/CodonUsageIndices.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/IsoelectricPoint.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/MeltingTemp.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/ProtParam.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/ProtParamData.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/lcc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/CheckSum.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/ProtParam.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/ProtParamData.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/IsoelectricPoint.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/CodonUsage.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/CodonUsageIndices.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/lcc.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SeqUtils/__pycache__/MeltingTemp.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Ace.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Phd.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications/_Novoalign.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications/_bwa.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications/_samtools.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications/__pycache__/_Novoalign.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications/__pycache__/_bwa.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/Applications/__pycache__/_samtools.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/__pycache__/Ace.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Sequencing/__pycache__/Phd.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat/FreqTable.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat/MatrixInfo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat/__pycache__/FreqTable.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SubsMat/__pycache__/MatrixInfo.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SVDSuperimposer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SVDSuperimposer/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SVDSuperimposer
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SVDSuperimposer/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SVDSuperimposer/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SVDSuperimposer/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SwissProt/KeyWList.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SwissProt/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SwissProt
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SwissProt/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SwissProt/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SwissProt/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/SwissProt/__pycache__/KeyWList.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SwissProt/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/TogoWS
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/TogoWS/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/TogoWS
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/TogoWS/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/TogoWS/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/TogoWS/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/BaseTree.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/CDAO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/CDAOIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Consensus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/NeXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/NeXMLIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Newick.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/NewickIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/NexusIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PhyloXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PhyloXMLIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/TreeConstruction.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/_cdao_owl.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/_io.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/_utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications/_Fasttree.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications/_Phyml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications/_Raxml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications/__pycache__/_Phyml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications/__pycache__/_Raxml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/Applications/__pycache__/_Fasttree.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/_paml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/_parse_baseml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/_parse_codeml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/_parse_yn00.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/baseml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/chi2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/codeml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/yn00.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/chi2.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/baseml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/_paml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/_parse_baseml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/codeml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/_parse_codeml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/yn00.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/PAML/__pycache__/_parse_yn00.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/_io.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/BaseTree.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/NewickIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/Newick.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/NexusIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/PhyloXMLIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/PhyloXML.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/NeXMLIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/NeXML.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/_cdao_owl.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/CDAOIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/CDAO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/_utils.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/TreeConstruction.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Phylo/__pycache__/Consensus.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniGene/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniGene
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniGene/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniGene/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniGene/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniProt/GOA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniProt/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniProt
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniProt/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniProt/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniProt/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/UniProt/__pycache__/GOA.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniProt/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise/dnal.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise/psw.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise/__pycache__/psw.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/Wise/__pycache__/dnal.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/cpairwise2module.c -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/cpairwise2.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/Seq.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/SeqRecord.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/File.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/SeqFeature.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/bgzf.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/LogisticRegression.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/MarkovModel.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/NaiveBayes.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/pairwise2.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/kNN.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/MaxEntropy.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Bio/__pycache__/_utils.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/BioSeq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/BioSeqDatabase.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/DBUtils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/Loader.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/__pycache__/BioSeqDatabase.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/__pycache__/BioSeq.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/__pycache__/Loader.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/BioSQL/__pycache__/DBUtils.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.config
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.config/matplotlib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.cache
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.cache/matplotlib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/home/.cache/matplotlib/fontlist-v330.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.cache/matplotlib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.t_coffee
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.t_coffee/cache
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.t_coffee/mcoffee
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.t_coffee/methods
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.t_coffee/plugins
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/home/.t_coffee/plugins/linux
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/ACT_example.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/PF05371_seed.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/Plates.csv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/Proux_et_al_2002_Figure_6.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/alpha.faa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/beta.faa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/clustal_run.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/ec_5.4.2.2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/fasta_dictionary.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/fasta_iterator.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/getgene.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/ls_orchid.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/ls_orchid.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/ls_orchid.gbk.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/ls_orchid.gbk.bz2 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/ls_orchid.gbk.gz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/m_cold.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/my_blast.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/my_blat.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/nmr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/nmr/noed.xpk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/nmr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/nmr/simplepredict.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/nmr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/opuntia.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/opuntia.dnd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/opuntia.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/simple.dnd -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/swissprot.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/examples/www_blast.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_advanced.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_align.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_appendix.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_blast.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_cluster.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_contributing.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_cookbook.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_entrez.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_graphics.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_introduction.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_kegg.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_learning.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_motifs.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_pdb.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_phenotype.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_phylo.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_popgen.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_quick_start.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_searchio.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_seq_annot.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_seq_objects.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_seqio.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_testing.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_uniprot.tex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_introduction.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_quick_start.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_seq_objects.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_seq_annot.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_seqio.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_align.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_blast.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_searchio.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_entrez.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_uniprot.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_pdb.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_popgen.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_phylo.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_motifs.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_cluster.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_learning.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_graphics.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_kegg.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_phenotype.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_cookbook.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_testing.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_advanced.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_contributing.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Doc/Tutorial/chapter_appendix.aux -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/Tutorial
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/.coveragerc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/310.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/3100.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/3730.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/A6_1-DB3.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/empty.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/fake.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/no_smpl1.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/nonascii_encoding.ab1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/test.fsa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Abi/test_data -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Abi
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Ace
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Ace/consed_sample.ace -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Ace
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Ace/contig1.ace -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Ace
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Ace/seq.cap.ace -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Ace
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Affy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Affy/affy_v3_example.CEL -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Affy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Affy/affy_v4_example.CEL -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Affy
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/bsubtilis.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/bsubtilis.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/cow.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/cow.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/ecoli.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/ecoli.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/hg38.chrom.sizes -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/pig.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Align/pig.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Align
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BWA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/BWA/HNSCC1_1_truncated.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BWA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/BWA/HNSCC1_2_truncated.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BWA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/BWA/human_g1k_v37_truncated.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BWA
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/BioSQL/biosqldb-mysql.sql -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/BioSQL/biosqldb-pg.sql -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/BioSQL/biosqldb-sqlite.sql -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BioSQL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/BioSQL/cor6_6.db -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/BioSQL
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mirna.tab -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mirna.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mock_actin.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mock_disco.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mock_orchid.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mock_pcr.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mock_short_empty.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mock_short_result.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/mock_wait.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_005.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_006.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_007.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_008.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_009.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_010.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_011.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_012.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2226_tblastn_013.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2228_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/tab_2228_tblastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastp_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastp_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastp_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastp_005.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastp_006.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastp_007.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_blastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_phiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_phiblast_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_phiblast_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_tblastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2010L_tblastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastp_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastp_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastp_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastp_005.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastp_006.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastp_007.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_blastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_phiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_phiblast_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_phiblast_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_tblastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2011L_tblastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2012L_psiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2014L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2014L_psiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2102L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2201L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2202L_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2202L_blastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2202L_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2208L_psiblast_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2215L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2216L_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2220L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2220L_blastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2221L_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2222L_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2222_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastp_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastp_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastp_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastx_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_blastx_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_tblastn_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_tblastn_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_tblastn_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_tblastn_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_tblastx_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_tblastx_002.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_tblastx_003.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2226_tblastx_004.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/text_2230_blastp_001.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/wnts.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/wnts.xml.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2212L_blastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2212L_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2212L_blastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2212L_tblastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2212L_tblastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2218L_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2218L_rpsblast_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2218_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2218_blastp_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2222_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2222_blastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastn_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastn_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastn_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastn_005.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastn_006.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastp_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastp_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastp_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastp_005.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastx_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastx_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_blastx_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastn_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastn_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastn_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastn_005.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastx_002.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastx_003.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2226_tblastx_004.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_blastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_blastn_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_blastp_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_blastp_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_blastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_blastx_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_tblastn_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_tblastn_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_tblastx_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/xml_2900_tblastx_001_v2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blast/html_msgid_29_blastx_001.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blast
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/mirna.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/psl_34_001.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/psl_34_002.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/psl_34_003.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/psl_34_004.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/psl_34_005.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/psl_35_001.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/psl_35_002.psl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/pslx_34_001.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/pslx_34_002.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/pslx_34_003.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/pslx_34_004.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/pslx_34_005.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Blat/pslx_35_002.pslx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Blat
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/CDAO
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/CDAO/test.cdao -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/CDAO
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Cellosaurus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Cellosaurus/cell_lines_1.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Cellosaurus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Cellosaurus/cell_lines_2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Cellosaurus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Cellosaurus/cell_lines_3.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Cellosaurus
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Clustalw/cw02.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Clustalw/hedgehog.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Clustalw/odd_consensus.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Clustalw/opuntia.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Clustalw/promals3d.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Clustalw/protein.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Clustalw
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Clustalw/temp horses.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Clustalw
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Cluster/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Cluster
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Cluster/cyano.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Cluster
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/CodonUsage
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/CodonUsage/HighlyExpressedGenes.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/CodonUsage
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Compass
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Compass/comtest1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Compass
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Compass/comtest2 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Compass
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/101ma_no_coords.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/A04195.imgt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/AAA03323.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/AE017046.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/DD231055_edited.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/DD231055_edited2.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/DS830848.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/Human_contigs.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/RepBase23.02.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/SC10H5.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/TRBG361.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/U87107.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/embl_with_0_line.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/epo_prt_selection.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/hla_3260_sample.imgt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/kipo_prt_sample.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/location_wrap.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/patents.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/EMBL/xx_after_co.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/EMBL
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/NirK.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/NirK_full.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/alignret.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/bac_find.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/bac_find.psearch -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/cds_forward.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/cds_reverse.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/emboss_pair_aln_full_blank_line.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/internal_oligo.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/matcher_pair.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/matcher_simple.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/needle.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/needle_asis.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/no_oligo.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/short.primer3 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/water.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Emboss/water2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Emboss
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/biosample.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/efetch_schemas.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/egquery1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/egquery2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/einfo1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/einfo2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/einfo3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/einfo4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/elink1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/elink2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/elink3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/elink4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/elink5.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/elink6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/elink7.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/elink8.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/epost1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/epost2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/epost3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esearch1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esearch2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esearch3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esearch4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esearch5.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esearch6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esearch7.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esearch8.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/espell.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary3.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary5.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary7.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary8.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/esummary9.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/journals.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/ncbi_mim.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/nucleotide1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/nucleotide2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/protein.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/pubmed1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/pubmed2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/pubmed3.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/pubmed4.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/pubmed5.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/pubmed6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/pubmed7.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Entrez/taxonomy.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Entrez
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Enzymes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Enzymes/lactate.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Enzymes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Enzymes/lipoprotein.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Enzymes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Enzymes/proline.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Enzymes
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Enzymes/valine.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Enzymes
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_affine_local.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_cdna2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_coding2coding.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_coding2coding_fshifts.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_coding2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_dna2protein.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_est2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_genome2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_ner.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_protein2dna.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_protein2dna_fshifts.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_protein2genome.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_ungapped.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_m_ungapped_trans.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_o_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_o_vulgar_cigar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_o_vulgar_fshifts.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_o_vulgar_fshifts2.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_q_multiple.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_q_multiple_vulgar.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Exonerate/exn_22_q_none.exn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Exonerate
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/ExtendedPhylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/ExtendedPhylip/primates.phyx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/ExtendedPhylip
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/FSSP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/FSSP/1cnv.fssp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/FSSP
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/aster.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/aster_no_wrap.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/centaurea.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/dups.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/elderberry.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/f001 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/f002 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/f003 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/fa01 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/flowers.pro.gz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/lavender.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/loveliesbleeding.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/lupine.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output001.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output002.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output003.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output004.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output005.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output006.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output007.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output008.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output009.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output010.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output011.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output012.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output013.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output014.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output015.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/output016.m10 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/phlox.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/rose.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/rosemary.pro -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/sweetpea.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/wisteria.nu -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Fasta/tc_out.msf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Fasta
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GFF/NC_001422.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GFF/NC_001802.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GFF/NC_001802lc.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GFF/NC_001802x.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GFF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GFF/multi.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GFF
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Gck
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Gck/artificial.gck -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Gck
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/1MRR_A.gp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/DS830848.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/EU851978.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/EU851978_output.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/GU949562.1.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/HM138502.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/HM138502_output.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/KF527485.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/KF527485_output.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NC_000932.faa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NC_000932.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NC_000932.gb.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NC_005816.faa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NC_005816.ffn -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NC_005816.fna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NC_005816.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NC_005816.tsv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NP_416719.gbwithparts -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/NT_019265.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/arab1.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/bad_loc_wrap.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/bad_origin_wrap.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/bad_origin_wrap_CDS.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/bad_origin_wrap_fuzzy.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/bad_origin_wrap_linear.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/blank_seq.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/cor6_6.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/cor6_6.gb.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/dbsource_wrap.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/empty_accession.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/empty_feature_qualifier.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/empty_version.gbk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/extra_keywords.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/gbvrl1_start.seq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/invalid_locus_line_spacing.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/invalid_misc_feature.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/invalid_product.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/invalid_structured_comment.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/iro.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/negative_location.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/no_end_marker.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/no_origin_no_end.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/noref.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/one_of.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/origin_line.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/pBAD30.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/pri1.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/protein_refseq.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/protein_refseq2.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/qualifier_escaping_read.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/qualifier_escaping_write.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/tls_KDHP01000000.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/tsa_acropora.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/GenBank/wrong_sequence_indent.gb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/GenBank
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/GSE16.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/GSM645.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/GSM691.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/GSM700.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/GSM804.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/soft_ex_affy.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/soft_ex_affy_chp.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/soft_ex_dual.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/soft_ex_family.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/soft_ex_platform.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Geo/soft_ex_series.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Geo
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/spiral_test.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/square_test.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_by_meth_linear.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_by_meth_circular.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_by_obj_circular.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_by_obj_frag_circular.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_by_obj_linear.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_by_obj_frag_linear.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_region_linear.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_region_linear.svg -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_region_circular.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_region_circular.svg -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/line_graph.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/line_graph_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/labels_default.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/labels_default_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigils.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigils_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_arrows.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_arrows_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_arrow_shafts.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_arrow_shafts_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_bigarrow_shafts.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_bigarrow_shafts_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_labels.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_labels_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_long_ARROW.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_long_ARROW_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_long_BIGARROW.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_long_BIGARROW_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_long_JAGGY.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_long_JAGGY_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_long_OCTO.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_long_OCTO_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_short_ARROW.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_short_ARROW_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_short_BIGARROW.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_short_BIGARROW_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_short_JAGGY.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_short_JAGGY_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_short_OCTO.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/GD_sigil_short_OCTO_c.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/random_organism.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/organism.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/organism.eps -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/organism.svg -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/tRNA_chrom_sf.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/tRNA_chrom.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/multi_bar.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/simple_bar.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/scatter_test_1.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/scatter_test_7.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/map01100_original.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/map03070_original.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/map01100_widths.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/map03070_colors.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/map01100_transparency.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Graphics/map03070_transparency.pdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Graphics
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/2uvo_hhblits.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/2uvo_hhblits_emptytable.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/2uvo_hhblits_onlyheader.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/2uvo_hhsearch.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/4p79_hhsearch_server_NOssm.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/4y9h_hhsearch_server_NOssm.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/allx.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/hhpred_9590198.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/HHsuite/hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/HHsuite
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/domtab_30_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/domtab_30_hmmscan_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/domtab_30_hmmscan_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/domtab_30_hmmscan_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/domtab_30_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/domtab_31b1_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/domtab_31b1_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/tab_30_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/tab_30_hmmscan_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/tab_30_hmmscan_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/tab_30_hmmscan_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/tab_31b1_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/tab_31b1_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_20_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_21_hmmpfam_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_22_hmmpfam_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_22_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_23_hmmpfam_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_23_hmmpfam_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_23_hmmpfam_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_23_hmmpfam_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_24_hmmpfam_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_005.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_006.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_007.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_008.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_009.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmscan_010.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmsearch_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmsearch_003.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmsearch_004.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_30_hmmsearch_005.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_31b1_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_31b1_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_31b2_hmmscan_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_31b2_hmmsearch_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_31b2_hmmsearch_002.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Hmmer/text_31b2_phmmer_001.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Hmmer
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/IntelliGenetics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/IntelliGenetics/TAT_mase_nuc.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/IntelliGenetics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/IntelliGenetics/VIF_mase-pro.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/IntelliGenetics
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/IntelliGenetics/vpu_nucaligned.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/IntelliGenetics
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/InterProScan
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/InterProScan/test_001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/InterProScan
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/compound.irregular -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/compound.sample -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/enzyme.4letter -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/enzyme.irregular -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/enzyme.new -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/enzyme.sample -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/gene.sample -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/ko00010.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/ko00253.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/ko01100.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/ko03070.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/map00950.rea -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/map01100.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/KEGG/map03070.png -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/KEGG
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/bug2453.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/bundle_without_target.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/cnksr3.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/corrupt.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/humor.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/invalid.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/length_coords_mismatch.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/ucsc_mm9_chr10.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/ucsc_mm9_chr10.mafindex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/ucsc_mm9_chr10_bad.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/ucsc_mm9_chr10_bad.mafindex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/ucsc_mm9_chr10_big.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/ucsc_mm9_chr10_big.mafindex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/ucsc_test.maf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/unfinished.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MAF/wrong_version.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MAF
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Mauve/simple.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Mauve/simple.xmfa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Mauve/simple.xmfa.backbone -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Mauve/simple.xmfa.bbcols -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Mauve
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Mauve/simple_short.xmfa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Mauve
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Medline
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Medline/pubmed_result1.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Medline
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Medline/pubmed_result2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Medline
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Medline/pubmed_result3.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Medline
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MetaTool/Meta3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MetaTool/Meta4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MetaTool/Meta6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MetaTool/Meta7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MetaTool/Meta8.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MetaTool/meta.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MetaTool/meta2.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/MetaTool/meta9.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/MetaTool
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NBRF/B_nuc.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NBRF/Cw_prot.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NBRF/DMA_nuc.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NBRF/DMB_prot.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NBRF
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NBRF/clustalw.pir -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NBRF
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NMR/noed.xpk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NMR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NMR/out_example.xpk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NMR
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/characters.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/edgelabels.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/meta_taxa.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/meta_types.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/nexml.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/phenoscape.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/sets.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/taxa.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/timetree.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/tolweb.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/treebase-record.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/trees-uris.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeXML/trees.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeXML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeuralNetwork
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeuralNetwork/enolase.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeuralNetwork
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/NeuralNetwork/repeat.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/NeuralNetwork
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/ByteOrderMarkFile.nwk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/bats.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/codonposset.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/int_node_labels.nwk -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/test.new -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/test_Nexus_input.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/vSysLab_Ganaspidium_multistate.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/vSysLab_Heptascelio_no-states_10+chars.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nexus/vSysLab_Oreiscelio_discrete+continuous.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nexus
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nib/test_even.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nib/test_even_bigendian.nib -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nib/test_even_littleendian.nib -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nib/test_odd.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nib/test_odd_bigendian.nib -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Nib/test_odd_littleendian.nib -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Nib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Alignments/aa_alignment.phylip -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Alignments/alignment.phylip -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Alignments/dottednames.phylip -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Alignments/dottednum.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Alignments/longnames.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Alignments
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Alignments/lysinYangSwanson2002.nuc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Alignments
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/bad1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/bad2.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/bad3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/SE.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/alpha1rho1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/baseml.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model0.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model2.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model4.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model5.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model6.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model7.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/model8.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/nhomo1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/nhomo3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/nhomo4.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/nparK1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/nparK2.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/nparK3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/baseml/nparK4.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/baseml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/NSsite3.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/SE.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/aa_model0.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/aa_pairwise.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/all_NSsites.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/branchsiteA.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/clademodelC.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/codeml.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/freeratio.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/m2a_rel.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/ngene2_mgene02.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/ngene2_mgene1.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/ngene2_mgene34.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/codeml/pairwise.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/codeml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/species.tree -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/yn00.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/yn00/yn00.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/yn00/yn00_dotted.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/yn00/yn00_dottednum.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Control_files/yn00/yn00_long.ctl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Control_files/yn00
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/bad_results.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/SE/SE-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/SE/SE-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/SE/SE-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/SE/SE-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/SE/SE-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/SE/SE-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/SE/SE-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/SE
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/alpha1rho1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/alpha1rho1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/alpha1rho1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/alpha1rho1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/baseml_SE.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/baseml_alpha1rho1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model0-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model0-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model0-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model0-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model0-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model0-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model0-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model1-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model1-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model1-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model1-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model1-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model1-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model1-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model2-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model2-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model2-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model2-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model2-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model2-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model2-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model3-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model3-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model3-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model3-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model3-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model3-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model3-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model4-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model4-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model4-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model4-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model4-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model4-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model4-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model5-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model5-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model5-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model5-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model5-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model5-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model5-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model6-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model6-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model6-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model6-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model6-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model6-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model6-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model7-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model7-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model7-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model7-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model7-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model7-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model7-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model8-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model8-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model8-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model8-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model8-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model8-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/model/model8-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/model
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo1-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo3-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nhomo/nhomo4-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nhomo
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK1-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK1-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK1-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK2-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK2-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK2-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK3-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK3-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK3-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK4-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK4-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/nparK/nparK4-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/nparK
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/versions
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/versions/baseml41.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/versions
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/versions/baseml43.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/versions
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/versions/baseml44.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/versions
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/baseml/versions/baseml44c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/baseml/versions
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/NSsite3
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/NSsite3/NSsite3-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/NSsite3
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/SE/SE-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/SE/SE-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/SE/SE-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/SE/SE-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/SE/SE-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/SE/SE-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/SE
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/SE/SE-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/SE
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_model0
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_model0/aa_model0-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_model0
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/aa_pairwise
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/all_NSsites
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/all_NSsites
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/branchsiteA
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/branchsiteA
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/clademodelC
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/clademodelC/clademodelC-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/clademodelC
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/freeratio
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/freeratio/freeratio-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/freeratio
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/m2a_rel
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/m2a_rel
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/m2a_rel
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_8.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/m2a_rel
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_9a.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/m2a_rel
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene02
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene1
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/ngene2_mgene34
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/pairwise/pairwise-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml/pairwise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/codeml/tree_regexp_versatility.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/codeml
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00-4_1.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00-4_3.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00-4_4.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00-4_4c.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00-4_5.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00-4_6.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00-4_7.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00-4_8.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00_dotted-4_9i.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00_dottednum-4_9i.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Results/yn00/yn00_long-4_8.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Results/yn00
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Trees/bad.tree -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Trees/lysin.trees -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Trees/lysin.trees.4.6 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/Trees/species.tree -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/Trees
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PAML/gen_results.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1A7G.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1A8O.asa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1A8O.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1A8O.mmtf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1A8O.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1A8O.rsa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1A8O.xyzr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1AS5.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1LCD.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1LCD.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1MOM_min.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1SSU_mod.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/1SSU_mod.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/2BEG.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/2BEG.dssp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/2BEG.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/2BEG_noheader.dssp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/2OFG.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/2XHE.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/2XHE.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/2n0n_M1.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/3JQH.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/4CUP.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/4CUP.mmtf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/4Q9R_min.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/4ZHL.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/4ZHL.mmtf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/Miller_RASA.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/Sander_RASA.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/Wilke_RASA.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/a_structure.cif -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/a_structure.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/alignment_file.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/d256ba_.ent -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/disordered.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/dssp_xtra_Sander.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/header.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/ions.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/lib_10_z_5.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PDB/occupancy.pdb -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PDB
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PQR
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PQR/1A80.pqr -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PQR
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phd
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phd/phd1 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phd
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phd/phd2 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phd
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phd/phd_454 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phd
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phd/phd_solexa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phd
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/hennigian.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/horses.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/horses.tree -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/interlaced.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/interlaced2.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/random.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/reference_dna.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/reference_dna2.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/sequential.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Phylip/sequential2.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Phylip
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PhyloXML/apaf.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PhyloXML/bcl_2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PhyloXML/distribution.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PhyloXML/example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PhyloXML/made_up.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PhyloXML/o_tol_332_d_dollo.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PhyloXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PhyloXML/phyloxml_examples.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PhyloXML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/big.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/c2line.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/c2space.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/c3line.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/c3space.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/haplo.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/haplo2.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/PopGen/haplo3.gen -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PopGen
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00100.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00113.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00144.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00149.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00340.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00424.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00472.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00640.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00787.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/pdoc00933.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/Doc/prosite.excerpt.doc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite/Doc
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/ps00107.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/ps00159.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/ps00165.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/ps00432.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/ps00488.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Prosite/ps00546.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Prosite
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_diff_ids.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_double_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_double_seq.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_long_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_no_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_qual_del.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_qual_escape.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_qual_null.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_qual_space.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_qual_tab.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_qual_unit_sep.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_qual_vtab.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_short_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_spaces.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_tabs.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_trunc_at_plus.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_trunc_at_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_trunc_at_seq.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_trunc_in_plus.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_trunc_in_qual.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_trunc_in_seq.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/error_trunc_in_title.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/example.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/example.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/example.fastq.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/example.fastq.gz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/example.qual -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/example_dos.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/example_dos.fastq.bgz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/illumina_faked.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/illumina_full_range_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/illumina_full_range_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/illumina_full_range_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/illumina_full_range_original_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/longreads_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/longreads_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/longreads_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/longreads_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/misc_dna_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/misc_dna_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/misc_dna_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/misc_dna_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/misc_rna_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/misc_rna_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/misc_rna_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/misc_rna_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/sanger_93.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/sanger_faked.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/sanger_full_range_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/sanger_full_range_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/sanger_full_range_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/sanger_full_range_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/solexa_example.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/solexa_faked.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/solexa_full_range_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/solexa_full_range_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/solexa_full_range_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/solexa_full_range_original_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/tricky.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/wrapping_as_illumina.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/wrapping_as_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/wrapping_as_solexa.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/wrapping_original_sanger.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Quality/zero_length.fastq -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Quality
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/bamii.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/bamii.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/cac81.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/cac81.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/crei.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/crei.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/foki.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/foki.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/pvuii.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/pvuii.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/taqi.htm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Rebase/taqi.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Rebase
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Registry
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Registry/EDD_RAT.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Registry
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Registry/bt001 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Registry
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Registry/seqs.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Registry
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_alt_index_at_end.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_alt_index_at_start.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_alt_index_in_middle.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_index_at_start.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_index_in_middle.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_no_manifest.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_random_10_reads.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_random_10_reads.qual -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_random_10_reads.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_random_10_reads.sff.gz -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_random_10_reads_no_trim.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/E3MFGYR02_random_10_reads_no_trim.qual -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/README.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/greek.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/invalid_greek_E3MFGYR02.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/invalid_paired_E3MFGYR02.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/paired.sff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/triple_sff.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Roche/triple_sff_rel_paths.idx -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Roche
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/dir.cla.scop.txt_test -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/dir.des.scop.txt_test -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/dir.hie.scop.txt_test -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/raftest.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-all-test.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-10-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-100-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-20-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-25-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-30-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-35-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-40-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-50-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-70-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-90-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-95-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+0,7-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+0-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+1-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-0,3-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-1,3-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-1-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-10-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-15-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-2,3-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-2-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-20-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-25-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-3-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-4-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-5-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-50-test.id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP/scopseq-test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SCOP/testDom.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SCOP
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Saf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Saf/saf1.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Saf
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/bam1.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/bam1_sorted.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/bam2.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/bam2_sorted.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/ex1.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/ex1.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/ex1.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/ex1_header.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/ex1_header.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/ex1_refresh.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/readme.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/sam1.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SamBam/sam2.sam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SamBam
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SeqXML/corrupt_example1.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SeqXML/corrupt_example2.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SeqXML/dna_example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SeqXML/global_species_example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SeqXML/protein_example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SeqXML
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SeqXML/rna_example.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SeqXML
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SnapGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SnapGene/pFA-KanMX4.dna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SnapGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SnapGene/sample-d.dna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SnapGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SnapGene/sample-e.dna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SnapGene
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Stockholm/funny.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Stockholm
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Stockholm/simple.sth -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Stockholm
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SubsMat/aaDistrib.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SubsMat/acc_rep_mat.pik -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SubsMat/protein_count.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SubsMat/protein_freq.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SubsMat/redAADistrib.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SubsMat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SubsMat/redAltAADistrib.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SubsMat
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/F2CXE6.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/F2CXE6.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/H2CNN8.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/H2CNN8.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/O23729.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/P0A186.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/P0CK95.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/P60137.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/P84001.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/P97881.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/Q13639.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/Q13639.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/R5HY77.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/README -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/keywlist.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/keywlist2.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/multi_ex.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/multi_ex.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/multi_ex.list -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/multi_ex.rdf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/multi_ex.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/multi_ex.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp001 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp002 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp003 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp005 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp006 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp007 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp008 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp009 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp010 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp011 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp012 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp013 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp015 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/sp016 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/uni001 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/uni002 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/SwissProt/uni003 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/SwissProt
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/adam_refs.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/consensus_refs.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/majority_ref.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/msa.phy -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/neighbor_trees.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/nj.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/nj_min.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/pars3.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/strict_refs.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/test.log -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/trees.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TreeConstruction/upgma.tre -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TreeConstruction
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TwoBit
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TwoBit/sequence.bigendian.2bit -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TwoBit
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TwoBit/sequence.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TwoBit
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TwoBit/sequence.littleendian.2bit -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TwoBit
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/TwoBit/sequence.long.2bit -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/TwoBit
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/UniGene/Eca.1.2425.data -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/UniGene/Hs.2.data -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniGene
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/UniGene/Mdm_partial.data -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniGene
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/UniProt/gene_association.goa_yeast.1.gaf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/UniProt/goa_human_sample.gpi -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/UniProt/goa_yeast.gaf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/UniProt/goa_yeast.gpa.59.gpa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniProt
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/UniProt/gp_information.goa_yeast.28.gpi -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/UniProt
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Wise/human_114_g01_exons.fna_01 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Wise
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Wise/human_114_g02_exons.fna_01 -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Wise
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Xdna
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Xdna/sample-a.xdna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Xdna
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Xdna/sample-b.xdna -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Xdna
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/Xdna/sample-c.xprt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/Xdna
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/biosql.ini.appveyor -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/biosql.ini.sample -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/adh.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/drosophilla.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/egfr_id -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/egfr_nucl.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/egfr_pro.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/nucl1.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/nucl2.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/nucl3.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/nucl4.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/nucl5.fa -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/pro1.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/pro2.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/pro3.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/pro4.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/codonalign/pro5.aln -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/codonalign
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/common_BioSQL.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/common_BioSQL_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/Arnt.sites -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/MA0056.1.transfac -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/REB1.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/SRF.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/abdb.xms -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/alignace.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/clusterbuster.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/clusterbuster.pfm.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/fourcolumns.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/fourrows.pfm -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.Klf1-200.cd.oops.xml.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.Klf1-200.cd.oops.xml.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.Klf1-200.cd.oops.xml.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.adh.de.oops.html.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.adh.de.oops.html.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.adh.de.oops.html.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.crp0.de.oops.txt.html -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.crp0.de.oops.txt.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/mast.crp0.de.oops.txt.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/meme.INO_up800.classic.oops.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/meme.adh.classic.oops.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/meme.farntrans5.classic.anr.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/meme.out -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/meme.psp_test.classic.zoops.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/minimal_test.meme -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/motifs/transfac.dat -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/motifs
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/msf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/msf/DOA_prot.msf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/msf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/msf/W_prot.msf -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/msf
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/pairwise2_testCases.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/phenotype/BadPlate.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/phenotype/Plate.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/phenotype/Plate_2.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/phenotype/Plates.csv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/phenotype/SmallPlate.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/phenotype/SmallPlate_2.json -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/phenotype/SmallPlates.csv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/phenotype
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/requires_internet.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/requires_wise.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/run_tests.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/search_tests_common.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/seq_tests_common.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Ace.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Affy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_AlignIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_AlignIO_ClustalIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_AlignIO_EmbossIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_AlignIO_FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_AlignIO_MauveIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_AlignIO_PhylipIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_AlignIO_convert.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_AlignInfo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Application.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_BWA_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_BioSQL_MySQLdb_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_BioSQL_mysql_connector.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_BioSQL_mysql_connector_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_BioSQL_psycopg2_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_BioSQL_sqlite3.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_BioSQL_sqlite3_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Blast_Record.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_CAPS.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Chi2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_ClustalOmega_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Clustalw_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Cluster.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_CodonTable.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_ColorSpiral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Compass.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Consensus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Dialign_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_EMBL_unittest.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Emboss.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_EmbossPrimer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Entrez.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Entrez_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Entrez_parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Enzyme.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_ExPASy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Fasttree_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_File.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_GenBank.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_GenomeDiagram.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_GraphicsChromosome.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_GraphicsDistribution.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_GraphicsGeneral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_HMMCasino.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_HMMGeneral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_KEGG.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_KEGG_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_KGML_graphics.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_KGML_graphics_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_KGML_nographics.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_KeyWList.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_LogisticRegression.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_MafIO_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Mafft_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_MarkovModel.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Medline.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Muscle_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NCBITextParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NCBIXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NCBI_qblast.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NMR.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NaiveBayes.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Nexus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PAML_baseml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PAML_codeml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PAML_yn00.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDBList.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_Dice.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_Disordered.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_Exposure.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_FragmentMapper.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_KDTree.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_MMCIF2Dict.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_MMCIFIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_MMCIFParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_NACCESS.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_PDBIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_PDBParser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_Polypeptide.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_SASA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_SMCRA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_StructureAlignment.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_Superimposer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_internal_coords.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_parse_pdb_header.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_vectors.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PQR.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Pathway.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Phd.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Phylo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PhyloXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Phylo_CDAO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Phylo_NeXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Phylo_matplotlib.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Phylo_networkx.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PopGen_GenePop_nodepend.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Prank_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Probcons_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_ProtParam.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_QCPSuperimposer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_RCSBFormats.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Restriction.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_Astral.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_Cla.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_Des.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_Dom.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_Hie.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_Raf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_Residues.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_Scop.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SCOP_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SVDSuperimposer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_blast_tab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_blast_tab_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_blast_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_blast_xml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_blast_xml_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_blat_psl.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_blat_psl_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_exonerate.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_exonerate_text_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_exonerate_vulgar_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_fasta_m10.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_fasta_m10_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hhsuite2_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hmmer2_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hmmer2_text_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hmmer3_domtab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hmmer3_domtab_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hmmer3_tab.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hmmer3_tab_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hmmer3_text.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_hmmer3_text_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_interproscan_xml.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_legacy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_model.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SearchIO_write.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqFeature.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_AbiIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_FastaIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_Gck.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_Insdc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_NibIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_PdbIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_QualityIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_SeqXML.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_SnapGene.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_TwoBitIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_Xdna.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_features.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_index.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqIO_write.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqRecord.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SeqUtils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Seq_objs.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SffIO.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SubsMat.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_SwissProt.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_TCoffee_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_TogoWS.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_TreeConstruction.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Tutorial.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_UniGene.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_UniProt_GOA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Uniprot.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_Wise.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_align.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_align_substitution_matrices.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_bgzf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_cellosaurus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_codonalign.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_geo.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_kNN.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_motifs.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_motifs_online.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_pairwise2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_pairwise2_no_C.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_pairwise_aligner.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_pairwise_alignment_map.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_phenotype.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_phenotype_fit.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_phyml_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_prodoc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_prosite.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_psw.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_samtools_tool.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_seq.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_translate.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_PDB_DSSP.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_GraphicsBitmaps.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/requires_internet.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Ace.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Affy.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_AlignIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_AlignIO_ClustalIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_AlignIO_EmbossIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_AlignIO_FastaIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_AlignIO_MauveIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_AlignIO_PhylipIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_AlignIO_convert.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_AlignInfo.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Application.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_BWA_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_BioSQL_MySQLdb_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/common_BioSQL.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/seq_tests_common.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/common_BioSQL_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_BioSQL_mysql_connector.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_BioSQL_mysql_connector_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_BioSQL_psycopg2_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_BioSQL_sqlite3.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_BioSQL_sqlite3_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Blast_Record.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_CAPS.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Chi2.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_ClustalOmega_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Clustalw_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Cluster.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_CodonTable.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_ColorSpiral.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Compass.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Consensus.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Dialign_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_EMBL_unittest.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Emboss.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_EmbossPrimer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Entrez.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Entrez_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Entrez_parser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Enzyme.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_ExPASy.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Fasttree_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_File.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_GenBank.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_GenomeDiagram.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_GraphicsBitmaps.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_GraphicsChromosome.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_GraphicsDistribution.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_GraphicsGeneral.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_HMMCasino.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_HMMGeneral.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_KEGG.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_KEGG_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_KGML_graphics.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_KGML_graphics_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_KGML_nographics.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_KeyWList.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_LogisticRegression.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_MafIO_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Mafft_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_MarkovModel.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Medline.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Muscle_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_NCBITextParser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_NCBIXML.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_NCBI_BLAST_tools.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_NCBI_qblast.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_NMR.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_NaiveBayes.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Nexus.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PAML_baseml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PAML_codeml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PAML_yn00.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDBList.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_DSSP.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_Dice.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_Disordered.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_Exposure.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_FragmentMapper.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_KDTree.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_MMCIF2Dict.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_MMCIFIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_MMCIFParser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_NACCESS.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_PDBIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_PDBParser.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_Polypeptide.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_SASA.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_SMCRA.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_StructureAlignment.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_Superimposer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_internal_coords.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_parse_pdb_header.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PDB_vectors.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PQR.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Pathway.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Phd.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Phylo.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PhyloXML.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Phylo_CDAO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Phylo_NeXML.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Phylo_matplotlib.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Phylo_networkx.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_PopGen_GenePop_nodepend.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Prank_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Probcons_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_ProtParam.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_QCPSuperimposer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_RCSBFormats.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Restriction.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_Astral.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_Cla.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_Des.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_Dom.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_Hie.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_Raf.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_Residues.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_Scop.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SCOP_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SVDSuperimposer.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_blast_tab.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_blast_tab_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/search_tests_common.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_blast_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_blast_xml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_blast_xml_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_blat_psl.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_blat_psl_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_exonerate.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_exonerate_text_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_exonerate_vulgar_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_fasta_m10.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_fasta_m10_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hhsuite2_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hmmer2_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hmmer2_text_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hmmer3_domtab.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hmmer3_domtab_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hmmer3_tab.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hmmer3_tab_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hmmer3_text.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_hmmer3_text_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_interproscan_xml.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_legacy.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_model.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SearchIO_write.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqFeature.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_AbiIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_FastaIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_Gck.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_Insdc.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_NibIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_PdbIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_QualityIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_SeqXML.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_SnapGene.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_TwoBitIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_Xdna.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_features.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_index.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqIO_write.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqRecord.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SeqUtils.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Seq_objs.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SffIO.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SubsMat.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_SwissProt.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_TCoffee_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_TogoWS.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_TreeConstruction.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Tutorial.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_UniGene.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_UniProt_GOA.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Uniprot.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_Wise.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/requires_wise.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_align.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_align_substitution_matrices.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_bgzf.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_cellosaurus.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_codonalign.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_geo.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_kNN.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_motifs.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_motifs_online.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_pairwise2.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/pairwise2_testCases.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_pairwise2_no_C.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_pairwise_aligner.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_pairwise_alignment_map.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_phenotype.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_phenotype_fit.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_phyml_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_prodoc.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_prosite.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_psw.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_samtools_tool.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_seq.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/__pycache__/test_translate.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/output.best.fas -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/output.best.nex -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/tmpdirprankmsaAN3XZc
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/tmpdirprankmsaopf7yj
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/out.bam -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/File.py to File.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/MarkovModel.py to MarkovModel.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Seq.py to Seq.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqFeature.py to SeqFeature.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqRecord.py to SeqRecord.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/_utils.py to _utils.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/bgzf.py to bgzf.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/kNN.py to kNN.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/pairwise2.py to pairwise2.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Affy/CelFile.py to CelFile.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Affy/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_ClustalOmega.py to _ClustalOmega.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_Clustalw.py to _Clustalw.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_Dialign.py to _Dialign.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_MSAProbs.py to _MSAProbs.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_Mafft.py to _Mafft.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_Muscle.py to _Muscle.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_Prank.py to _Prank.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_Probcons.py to _Probcons.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/_TCoffee.py to _TCoffee.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/Applications/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/AlignIO/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Alphabet/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Application/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/Applications.py to Applications.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/ParseBlastTable.py to ParseBlastTable.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/Record.py to Record.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Blast/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/CAPS/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Cluster/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/chisq.py to chisq.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/codonalign/codonseq.py to codonseq.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Compass/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/CodonTable.py to CodonTable.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/IUPACData.py to IUPACData.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/SCOPData.py to SCOPData.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Data/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/Applications.py to Applications.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/Primer3.py to Primer3.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Emboss/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/Parser.py to Parser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Entrez/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/Record.py to Record.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/Scanner.py to Scanner.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/GenBank/utils.py to utils.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Geo/Record.py to Record.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Geo/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/Comparative.py to Comparative.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/Distribution.py to Distribution.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/DynamicProgramming.py to DynamicProgramming.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/MarkovModel.py to MarkovModel.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/Trainer.py to Trainer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/Utilities.py to Utilities.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/HMM/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/REST.py to REST.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Compound/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Enzyme/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Gene/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/Map/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML/KGML_parser.py to KGML_parser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML/KGML_pathway.py to KGML_pathway.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/KEGG/KGML/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf/DefaultParser.py to DefaultParser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmtf/mmtfio.py to mmtfio.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/AbstractPropertyMap.py to AbstractPropertyMap.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Atom.py to Atom.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Chain.py to Chain.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Dice.py to Dice.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Entity.py to Entity.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/FragmentMapper.py to FragmentMapper.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/HSExposure.py to HSExposure.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/MMCIF2Dict.py to MMCIF2Dict.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/MMCIFParser.py to MMCIFParser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Model.py to Model.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/NACCESS.py to NACCESS.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/NeighborSearch.py to NeighborSearch.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/PDBExceptions.py to PDBExceptions.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/PDBIO.py to PDBIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/PDBList.py to PDBList.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/PDBParser.py to PDBParser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/PICIO.py to PICIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/PSEA.py to PSEA.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Polypeptide.py to Polypeptide.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Residue.py to Residue.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/ResidueDepth.py to ResidueDepth.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/SASA.py to SASA.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/SCADIO.py to SCADIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Selection.py to Selection.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Structure.py to Structure.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/StructureAlignment.py to StructureAlignment.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/StructureBuilder.py to StructureBuilder.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/Superimposer.py to Superimposer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/ic_data.py to ic_data.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/ic_rebuild.py to ic_rebuild.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/internal_coords.py to internal_coords.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/mmcifio.py to mmcifio.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/parse_pdb_header.py to parse_pdb_header.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/vectors.py to vectors.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/DSSP.py to DSSP.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PDB/QCPSuperimposer/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Medline/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/alignace.py to alignace.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/clusterbuster.py to clusterbuster.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/mast.py to mast.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/matrix.py to matrix.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/meme.py to meme.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/minimal.py to minimal.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/pfm.py to pfm.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/thresholds.py to thresholds.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/transfac.py to transfac.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/xms.py to xms.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/applications/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/applications/_xxmotif.py to _xxmotif.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/jaspar/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/motifs/jaspar/db.py to db.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/Nexus.py to Nexus.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/Nodes.py to Nodes.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/StandardData.py to StandardData.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/Trees.py to Trees.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Nexus/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR/NOEtools.py to NOEtools.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/NMR/xpktools.py to xpktools.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep/Graph.py to Graph.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep/MultiGraph.py to MultiGraph.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Pathway/Rep/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/Controller.py to Controller.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/PrintFormat.py to PrintFormat.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/Restriction.py to Restriction.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Restriction/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/Cla.py to Cla.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/Des.py to Des.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/Dom.py to Dom.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/Hie.py to Hie.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/Raf.py to Raf.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/Residues.py to Residues.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SCOP/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_index.py to _index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_utils.py to _utils.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy/NCBIStandalone.py to NCBIStandalone.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy/ParserSupport.py to ParserSupport.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_legacy/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/_base.py to _base.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/hit.py to hit.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/_model/query.py to query.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/blast_text.py to blast_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py to hhsuite2_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqIO/_index.py to _index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SeqUtils/lcc.py to lcc.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Ace.py to Ace.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Phd.py to Phd.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat/FreqTable.py to FreqTable.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat/MatrixInfo.py to MatrixInfo.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SubsMat/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/SwissProt/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/TogoWS/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/CDAO.py to CDAO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Consensus.py to Consensus.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/NeXML.py to NeXML.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Newick.py to Newick.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/_io.py to _io.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/_utils.py to _utils.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniGene/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniProt/GOA.py to GOA.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/UniProt/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise/dnal.py to dnal.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Bio/Wise/psw.py to psw.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/BioSeq.py to BioSeq.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/DBUtils.py to DBUtils.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/Loader.py to Loader.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/BioSQL/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/ACT_example.py to ACT_example.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/Proux_et_al_2002_Figure_6.py to Proux_et_al_2002_Figure_6.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/clustal_run.py to clustal_run.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/fasta_dictionary.py to fasta_dictionary.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/fasta_iterator.py to fasta_iterator.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/getgene.py to getgene.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/nmr/simplepredict.py to simplepredict.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/swissprot.py to swissprot.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Doc/examples/www_blast.py to www_blast.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/PAML/gen_results.py to gen_results.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/common_BioSQL.py to common_BioSQL.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/common_BioSQL_online.py to common_BioSQL_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/pairwise2_testCases.py to pairwise2_testCases.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/requires_internet.py to requires_internet.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/requires_wise.py to requires_wise.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/run_tests.py to run_tests.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/search_tests_common.py to search_tests_common.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/seq_tests_common.py to seq_tests_common.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Ace.py to test_Ace.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Affy.py to test_Affy.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_AlignIO.py to test_AlignIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_AlignIO_ClustalIO.py to test_AlignIO_ClustalIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_AlignIO_EmbossIO.py to test_AlignIO_EmbossIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_AlignIO_FastaIO.py to test_AlignIO_FastaIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_AlignIO_MauveIO.py to test_AlignIO_MauveIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_AlignIO_PhylipIO.py to test_AlignIO_PhylipIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_AlignIO_convert.py to test_AlignIO_convert.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_AlignInfo.py to test_AlignInfo.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Application.py to test_Application.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_BWA_tool.py to test_BWA_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_BioSQL_MySQLdb_online.py to test_BioSQL_MySQLdb_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_BioSQL_mysql_connector.py to test_BioSQL_mysql_connector.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_BioSQL_mysql_connector_online.py to test_BioSQL_mysql_connector_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_BioSQL_psycopg2_online.py to test_BioSQL_psycopg2_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_BioSQL_sqlite3.py to test_BioSQL_sqlite3.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_BioSQL_sqlite3_online.py to test_BioSQL_sqlite3_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Blast_Record.py to test_Blast_Record.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_CAPS.py to test_CAPS.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Chi2.py to test_Chi2.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_ClustalOmega_tool.py to test_ClustalOmega_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Clustalw_tool.py to test_Clustalw_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Cluster.py to test_Cluster.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_CodonTable.py to test_CodonTable.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_ColorSpiral.py to test_ColorSpiral.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Compass.py to test_Compass.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Consensus.py to test_Consensus.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Dialign_tool.py to test_Dialign_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_EMBL_unittest.py to test_EMBL_unittest.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Emboss.py to test_Emboss.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_EmbossPrimer.py to test_EmbossPrimer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Entrez.py to test_Entrez.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Entrez_online.py to test_Entrez_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Entrez_parser.py to test_Entrez_parser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Enzyme.py to test_Enzyme.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_ExPASy.py to test_ExPASy.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Fasttree_tool.py to test_Fasttree_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_File.py to test_File.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_GenBank.py to test_GenBank.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_GenomeDiagram.py to test_GenomeDiagram.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_GraphicsChromosome.py to test_GraphicsChromosome.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_GraphicsDistribution.py to test_GraphicsDistribution.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_GraphicsGeneral.py to test_GraphicsGeneral.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_HMMCasino.py to test_HMMCasino.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_HMMGeneral.py to test_HMMGeneral.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_KEGG.py to test_KEGG.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_KEGG_online.py to test_KEGG_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_KGML_graphics.py to test_KGML_graphics.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_KGML_graphics_online.py to test_KGML_graphics_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_KGML_nographics.py to test_KGML_nographics.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_KeyWList.py to test_KeyWList.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_LogisticRegression.py to test_LogisticRegression.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_MafIO_index.py to test_MafIO_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Mafft_tool.py to test_Mafft_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_MarkovModel.py to test_MarkovModel.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Medline.py to test_Medline.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Muscle_tool.py to test_Muscle_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_NCBITextParser.py to test_NCBITextParser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_NCBIXML.py to test_NCBIXML.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_NCBI_BLAST_tools.py to test_NCBI_BLAST_tools.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_NCBI_qblast.py to test_NCBI_qblast.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_NMR.py to test_NMR.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_NaiveBayes.py to test_NaiveBayes.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Nexus.py to test_Nexus.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PAML_baseml.py to test_PAML_baseml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PAML_codeml.py to test_PAML_codeml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PAML_yn00.py to test_PAML_yn00.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDBList.py to test_PDBList.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_Dice.py to test_PDB_Dice.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_Disordered.py to test_PDB_Disordered.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_Exposure.py to test_PDB_Exposure.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_FragmentMapper.py to test_PDB_FragmentMapper.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_KDTree.py to test_PDB_KDTree.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_MMCIF2Dict.py to test_PDB_MMCIF2Dict.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_MMCIFIO.py to test_PDB_MMCIFIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_MMCIFParser.py to test_PDB_MMCIFParser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_NACCESS.py to test_PDB_NACCESS.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_PDBIO.py to test_PDB_PDBIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_PDBParser.py to test_PDB_PDBParser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_Polypeptide.py to test_PDB_Polypeptide.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_SASA.py to test_PDB_SASA.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_SMCRA.py to test_PDB_SMCRA.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_StructureAlignment.py to test_PDB_StructureAlignment.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_Superimposer.py to test_PDB_Superimposer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_internal_coords.py to test_PDB_internal_coords.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_parse_pdb_header.py to test_PDB_parse_pdb_header.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_vectors.py to test_PDB_vectors.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PQR.py to test_PQR.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Pathway.py to test_Pathway.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Phd.py to test_Phd.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Phylo.py to test_Phylo.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PhyloXML.py to test_PhyloXML.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Phylo_CDAO.py to test_Phylo_CDAO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Phylo_NeXML.py to test_Phylo_NeXML.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Phylo_matplotlib.py to test_Phylo_matplotlib.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Phylo_networkx.py to test_Phylo_networkx.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PopGen_GenePop_nodepend.py to test_PopGen_GenePop_nodepend.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Prank_tool.py to test_Prank_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Probcons_tool.py to test_Probcons_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_ProtParam.py to test_ProtParam.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_QCPSuperimposer.py to test_QCPSuperimposer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_RCSBFormats.py to test_RCSBFormats.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Restriction.py to test_Restriction.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_Astral.py to test_SCOP_Astral.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_Cla.py to test_SCOP_Cla.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_Des.py to test_SCOP_Des.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_Dom.py to test_SCOP_Dom.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_Hie.py to test_SCOP_Hie.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_Raf.py to test_SCOP_Raf.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_Residues.py to test_SCOP_Residues.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_Scop.py to test_SCOP_Scop.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SCOP_online.py to test_SCOP_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SVDSuperimposer.py to test_SVDSuperimposer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_blast_tab.py to test_SearchIO_blast_tab.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_blast_tab_index.py to test_SearchIO_blast_tab_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_blast_text.py to test_SearchIO_blast_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_blast_xml.py to test_SearchIO_blast_xml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_blast_xml_index.py to test_SearchIO_blast_xml_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_blat_psl.py to test_SearchIO_blat_psl.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_blat_psl_index.py to test_SearchIO_blat_psl_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_exonerate.py to test_SearchIO_exonerate.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_exonerate_text_index.py to test_SearchIO_exonerate_text_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_exonerate_vulgar_index.py to test_SearchIO_exonerate_vulgar_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_fasta_m10.py to test_SearchIO_fasta_m10.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_fasta_m10_index.py to test_SearchIO_fasta_m10_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hhsuite2_text.py to test_SearchIO_hhsuite2_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hmmer2_text.py to test_SearchIO_hmmer2_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hmmer2_text_index.py to test_SearchIO_hmmer2_text_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hmmer3_domtab.py to test_SearchIO_hmmer3_domtab.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hmmer3_domtab_index.py to test_SearchIO_hmmer3_domtab_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hmmer3_tab.py to test_SearchIO_hmmer3_tab.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hmmer3_tab_index.py to test_SearchIO_hmmer3_tab_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hmmer3_text.py to test_SearchIO_hmmer3_text.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_hmmer3_text_index.py to test_SearchIO_hmmer3_text_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_interproscan_xml.py to test_SearchIO_interproscan_xml.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_legacy.py to test_SearchIO_legacy.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_model.py to test_SearchIO_model.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SearchIO_write.py to test_SearchIO_write.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqFeature.py to test_SeqFeature.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO.py to test_SeqIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_AbiIO.py to test_SeqIO_AbiIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_FastaIO.py to test_SeqIO_FastaIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_Gck.py to test_SeqIO_Gck.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_Insdc.py to test_SeqIO_Insdc.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_NibIO.py to test_SeqIO_NibIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_PdbIO.py to test_SeqIO_PdbIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_QualityIO.py to test_SeqIO_QualityIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_SeqXML.py to test_SeqIO_SeqXML.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_SnapGene.py to test_SeqIO_SnapGene.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_TwoBitIO.py to test_SeqIO_TwoBitIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_Xdna.py to test_SeqIO_Xdna.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_features.py to test_SeqIO_features.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_index.py to test_SeqIO_index.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_online.py to test_SeqIO_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqIO_write.py to test_SeqIO_write.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqRecord.py to test_SeqRecord.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SeqUtils.py to test_SeqUtils.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Seq_objs.py to test_Seq_objs.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SffIO.py to test_SffIO.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SubsMat.py to test_SubsMat.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_SwissProt.py to test_SwissProt.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_TCoffee_tool.py to test_TCoffee_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_TogoWS.py to test_TogoWS.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_TreeConstruction.py to test_TreeConstruction.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Tutorial.py to test_Tutorial.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_UniGene.py to test_UniGene.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_UniProt_GOA.py to test_UniProt_GOA.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Uniprot.py to test_Uniprot.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_Wise.py to test_Wise.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_align.py to test_align.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_align_substitution_matrices.py to test_align_substitution_matrices.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_bgzf.py to test_bgzf.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_cellosaurus.py to test_cellosaurus.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_codonalign.py to test_codonalign.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_geo.py to test_geo.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_kNN.py to test_kNN.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_motifs.py to test_motifs.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_motifs_online.py to test_motifs_online.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_pairwise2.py to test_pairwise2.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_pairwise2_no_C.py to test_pairwise2_no_C.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_pairwise_aligner.py to test_pairwise_aligner.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_pairwise_alignment_map.py to test_pairwise_alignment_map.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_phenotype.py to test_phenotype.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_phenotype_fit.py to test_phenotype_fit.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_phyml_tool.py to test_phyml_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_prodoc.py to test_prodoc.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_prosite.py to test_prosite.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_psw.py to test_psw.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_samtools_tool.py to test_samtools_tool.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_seq.py to test_seq.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_translate.py to test_translate.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_PDB_DSSP.py to test_PDB_DSSP.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/Tests/test_GraphicsBitmaps.py to test_GraphicsBitmaps.cpython-39.pyc
running install_egg_info
Copying biopython.egg-info to /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/biopython-1.79.egg-info
Skipping SOURCES.txt
running install_scripts
dh_numpy3 -ppython3-biopython
	(grep -a -s -v python3:Depends debian/python3-biopython.substvars; echo "python3:Depends=python3-numpy (>= 1:1.16.0~rc1), python3-numpy-abi9") > debian/python3-biopython.substvars.new
	mv debian/python3-biopython.substvars.new debian/python3-biopython.substvars
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -a -O--buildsystem=pybuild
	install -d debian/python3-biopython//usr/lib/python3.9/dist-packages
	cp --reflink=auto -a debian/tmp/usr/lib/python3.9/dist-packages/Bio debian/tmp/usr/lib/python3.9/dist-packages/biopython-1.79.egg-info debian/python3-biopython//usr/lib/python3.9/dist-packages/
	install -d debian/.debhelper/generated/python3-biopython
	install -d debian/.debhelper/generated/python-biopython-doc
	install -d debian/.debhelper/generated/python3-biopython-sql
   dh_installdocs -a -O--buildsystem=pybuild
	install -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 -p -m0644 debian/changelog debian/python3-biopython/usr/share/doc/python3-biopython/changelog.Debian
   dh_python3 -a -O--buildsystem=pybuild
D: dh_python3 dh_python3:161: version: 5.20211016.1
D: dh_python3 dh_python3:162: argv: ['/usr/bin/dh_python3', '-a', '-O--buildsystem=pybuild']
D: dh_python3 dh_python3:163: options: {'guess_deps': True, 'skip_private': False, 'verbose': False, 'arch': True, 'package': None, 'no_package': None, '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, 'O': '--buildsystem=pybuild'}
D: dh_python3 dh_python3:164: args: []
D: dh_python3 dh_python3:165: supported Python versions: 3.9 (default=3.9)
D: dh_python3 debhelper:107: skipping package: python-biopython-doc
D: dh_python3 debhelper:152: source=python-biopython, binary packages=['python3-biopython']
D: dh_python3 dh_python3:183: processing package python3-biopython...
D: dh_python3 fs:49: moving files from debian/python3-biopython/usr/lib/python3.9/dist-packages to debian/python3-biopython/usr/lib/python3/dist-packages/
D: dh_python3 fs:265: package python3-biopython details = {'requires.txt': {'debian/python3-biopython/usr/lib/python3/dist-packages/biopython-1.79.egg-info/requires.txt'}, 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.9')}, 'ext_no_version': set()}
D: dh_python3 depends:118: generating dependencies for package python3-biopython
D: dh_python3 pydist:142: trying to find dependency for numpy (python=None)
D: dh_python3 depends:282: D={'python3 (>= 3.9~)', 'python3 (<< 3.10)', 'python3-numpy', 'python3:any'}; R=[]; S=[]; E=[], B=[]; RT=[]
   dh_installsystemduser -a -O--buildsystem=pybuild
   dh_lintian -a -O--buildsystem=pybuild
	install -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
	rm -f debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd
	ln -s ../../../../../../share/xml/schema/w3c/mathml/dtd/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/CONTRIBUTING.rst usr/share/doc/python3-biopython/DEPRECATED.rst 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/CONTRIBUTING.rst usr/share/doc/python3-biopython/DEPRECATED.rst 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 -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-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-39-arm-linux-gnueabihf.so
	objcopy --compress-debug-sections debian/python3-biopython/usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-biopython.debug
   dh_strip -a -O--buildsystem=pybuild
	install -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/b4
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-39-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/b4/d4bccc0d9f2ef168ad149e2101d70c4c60155e.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/b4/d4bccc0d9f2ef168ad149e2101d70c4c60155e.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-39-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/b4/d4bccc0d9f2ef168ad149e2101d70c4c60155e.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-39-arm-linux-gnueabihf.so
	install -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/7e
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-39-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/7e/e0a89918240eab79deb8b814f7f5bd52b41855.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/7e/e0a89918240eab79deb8b814f7f5bd52b41855.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-39-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/7e/e0a89918240eab79deb8b814f7f5bd52b41855.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-39-arm-linux-gnueabihf.so
	install -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/9d
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-39-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/9d/14e3e423364b7ebeb5729e1afff5fd1af21882.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/9d/14e3e423364b7ebeb5729e1afff5fd1af21882.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-39-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/9d/14e3e423364b7ebeb5729e1afff5fd1af21882.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-39-arm-linux-gnueabihf.so
	install -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/7f
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-39-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/7f/43ff03f4263fa2ac69efed2b206a9d5e4c477b.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/7f/43ff03f4263fa2ac69efed2b206a9d5e4c477b.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-39-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/7f/43ff03f4263fa2ac69efed2b206a9d5e4c477b.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-39-arm-linux-gnueabihf.so
	install -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/80
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/80/859cc4fb508b2b287cc52f228c83a8e8324909.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/80/859cc4fb508b2b287cc52f228c83a8e8324909.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/80/859cc4fb508b2b287cc52f228c83a8e8324909.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-arm-linux-gnueabihf.so
	install -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/51
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-39-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/51/c438816490ec44864785e74b0f178a5a2d5d17.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/51/c438816490ec44864785e74b0f178a5a2d5d17.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-39-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/51/c438816490ec44864785e74b0f178a5a2d5d17.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-39-arm-linux-gnueabihf.so
	install -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/d2
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-39-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/d2/e8988139082ab0a00c6c562ddceaca6e161b80.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/d2/e8988139082ab0a00c6c562ddceaca6e161b80.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-39-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/d2/e8988139082ab0a00c6c562ddceaca6e161b80.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-39-arm-linux-gnueabihf.so
	install -d debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/44
	objcopy --only-keep-debug --compress-debug-sections debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-39-arm-linux-gnueabihf.so debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/44/7830dcb41bc93e852eeabe27a76ead035663bd.debug
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/44/7830dcb41bc93e852eeabe27a76ead035663bd.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-39-arm-linux-gnueabihf.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-biopython/dbgsym-root/usr/lib/debug/.build-id/44/7830dcb41bc93e852eeabe27a76ead035663bd.debug debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-39-arm-linux-gnueabihf.so
	install -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 -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
   dh_makeshlibs -a -O--buildsystem=pybuild
	rm -f debian/python3-biopython/DEBIAN/shlibs
   dh_shlibdeps -a -O--buildsystem=pybuild
	install -d debian/python3-biopython/DEBIAN
	dpkg-shlibdeps -Tdebian/python3-biopython.substvars debian/python3-biopython/usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-39-arm-linux-gnueabihf.so debian/python3-biopython/usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-39-arm-linux-gnueabihf.so
   dh_installdeb -a -O--buildsystem=pybuild
	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
	echo misc:Depends= >> debian/python3-biopython.substvars
	echo misc:Pre-Depends= >> debian/python3-biopython.substvars
	install -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=447830dcb41bc93e852eeabe27a76ead035663bd 51c438816490ec44864785e74b0f178a5a2d5d17 7ee0a89918240eab79deb8b814f7f5bd52b41855 7f43ff03f4263fa2ac69efed2b206a9d5e4c477b 80859cc4fb508b2b287cc52f228c83a8e8324909 9d14e3e423364b7ebeb5729e1afff5fd1af21882 b4d4bccc0d9f2ef168ad149e2101d70c4c60155e d2e8988139082ab0a00c6c562ddceaca6e161b80" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: package python3-biopython: substitution variable ${python3:Provides} unused, but is defined
dpkg-gencontrol: warning: package python3-biopython: substitution variable ${python3:Versions} unused, but is defined
	chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -ppython3-biopython -ldebian/changelog -Tdebian/python3-biopython.substvars -Pdebian/python3-biopython
dpkg-gencontrol: warning: package python3-biopython: substitution variable ${python3:Provides} unused, but is defined
dpkg-gencontrol: warning: package python3-biopython: substitution variable ${python3:Versions} unused, but is defined
	chmod 0644 -- debian/python3-biopython/DEBIAN/control
   dh_md5sums -a -O--buildsystem=pybuild
	cd debian/python3-biopython >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/python3-biopython/DEBIAN/md5sums
	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_1.79+dfsg-1_armhf.deb'.
dpkg-deb: building package 'python3-biopython' in '../python3-biopython_1.79+dfsg-1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../python-biopython_1.79+dfsg-1_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 2021-10-25T07:35:23Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


python-biopython_1.79+dfsg-1_armhf.changes:
-------------------------------------------

Format: 1.8
Date: Fri, 22 Oct 2021 18:10:48 +0200
Source: python-biopython
Binary: python3-biopython python3-biopython-dbgsym
Architecture: armhf
Version: 1.79+dfsg-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
 python3-biopython - Python3 library for bioinformatics
Changes:
 python-biopython (1.79+dfsg-1) unstable; urgency=medium
 .
   * Migrate from Experimental to Unstable.
   * Mark spelling.patch as not needing forward.
     It seems that the file being package might not exists in upcoming
     Biopython versions anymore.
   * adjust-test_GraphicsBitmaps.patch: forwarded upstream.
   * d/control: breaks ncbi-acc-download (<< 0.2.7-2~)
Checksums-Sha1:
 43d5050bb1fe650a90830368e454a2b220219a87 11051 python-biopython_1.79+dfsg-1_armhf.buildinfo
 728a630ca7d8af2b191cb6254456ecd2f6b269d5 260228 python3-biopython-dbgsym_1.79+dfsg-1_armhf.deb
 8641dc2b4f2e6b672fc8e81fc7f3201020a90729 1400316 python3-biopython_1.79+dfsg-1_armhf.deb
Checksums-Sha256:
 b279963f8638d1539612f839ef2f101dc819bd53785ebd19167c1194483a5aa7 11051 python-biopython_1.79+dfsg-1_armhf.buildinfo
 8595c7dfbfdce44caedab99741c8cf61acb1e8bf6f7b49660dafa436672bbcd2 260228 python3-biopython-dbgsym_1.79+dfsg-1_armhf.deb
 2a3ead1eb5367b19bf706adf212359f6f9c136f9892811be788c02565b5afeab 1400316 python3-biopython_1.79+dfsg-1_armhf.deb
Files:
 6747484708dbd52d0142cc849a367f84 11051 python optional python-biopython_1.79+dfsg-1_armhf.buildinfo
 14ab5ed1d1febc0d6e988a1382123c06 260228 debug optional python3-biopython-dbgsym_1.79+dfsg-1_armhf.deb
 0664ce65bc64983834f6b1236907952a 1400316 python optional python3-biopython_1.79+dfsg-1_armhf.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: python-biopython
Binary: python3-biopython python3-biopython-dbgsym
Architecture: armhf
Version: 1.79+dfsg-1
Checksums-Md5:
 14ab5ed1d1febc0d6e988a1382123c06 260228 python3-biopython-dbgsym_1.79+dfsg-1_armhf.deb
 0664ce65bc64983834f6b1236907952a 1400316 python3-biopython_1.79+dfsg-1_armhf.deb
Checksums-Sha1:
 728a630ca7d8af2b191cb6254456ecd2f6b269d5 260228 python3-biopython-dbgsym_1.79+dfsg-1_armhf.deb
 8641dc2b4f2e6b672fc8e81fc7f3201020a90729 1400316 python3-biopython_1.79+dfsg-1_armhf.deb
Checksums-Sha256:
 8595c7dfbfdce44caedab99741c8cf61acb1e8bf6f7b49660dafa436672bbcd2 260228 python3-biopython-dbgsym_1.79+dfsg-1_armhf.deb
 2a3ead1eb5367b19bf706adf212359f6f9c136f9892811be788c02565b5afeab 1400316 python3-biopython_1.79+dfsg-1_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 25 Oct 2021 07:35:22 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.71-2),
 automake (= 1:1.16.5-1),
 autopoint (= 0.21-4),
 autotools-dev (= 20180224.1+nmu1),
 base-files (= 12+rpi1),
 base-passwd (= 3.5.51),
 bash (= 5.1-3),
 binutils (= 2.37-5+rpi1),
 binutils-arm-linux-gnueabihf (= 2.37-5+rpi1),
 binutils-common (= 2.37-5+rpi1),
 bsdextrautils (= 2.37.2-3),
 bsdutils (= 1:2.37.2-1),
 build-essential (= 12.9),
 bwa (= 0.7.17-6),
 bzip2 (= 1.0.8-4),
 clustalo (= 1.2.4-7),
 clustalw (= 2.1+lgpl-7),
 coreutils (= 8.32-4),
 cpp (= 4:10.2.1-1+rpi1),
 cpp-10 (= 10.3.0-9+rpi1),
 dash (= 0.5.11+git20210120+802ebd4-1),
 debconf (= 1.5.77),
 debhelper (= 13.5.2),
 debianutils (= 4.11.2),
 dh-autoreconf (= 20),
 dh-python (= 5.20211016.1),
 dh-strip-nondeterminism (= 1.12.0-2),
 dialign (= 2.2.1-11),
 diffutils (= 1:3.7-5),
 dpkg (= 1.20.9+rpi1),
 dpkg-dev (= 1.20.9+rpi1),
 dssp (= 4.0.0-2),
 dwz (= 0.14-1),
 emboss (= 6.6.0+dfsg-9),
 emboss-data (= 6.6.0+dfsg-9),
 emboss-lib (= 6.6.0+dfsg-9),
 fasttree (= 2.1.11-2),
 file (= 1:5.39-3),
 findutils (= 4.8.0-1),
 flex (= 2.6.4-8),
 fontconfig-config (= 2.13.1-4.2),
 fonts-lmodern (= 2.004.5-6.1),
 fonts-lyx (= 2.3.6-1),
 fonts-urw-base35 (= 20200910-1),
 g++ (= 4:10.2.1-1+rpi1),
 g++-10 (= 10.3.0-9+rpi1),
 gcc (= 4:10.2.1-1+rpi1),
 gcc-10 (= 10.3.0-9+rpi1),
 gcc-10-base (= 10.3.0-9+rpi1),
 gcc-11-base (= 11.2.0-9+rpi1),
 gettext (= 0.21-4),
 gettext-base (= 0.21-4),
 ghostscript (= 9.54.0~dfsg-5),
 grep (= 3.7-1),
 groff-base (= 1.22.4-7),
 gzip (= 1.10-4),
 hevea (= 2.35-1),
 hostname (= 3.23),
 init-system-helpers (= 1.60),
 intltool-debian (= 0.35.0+20060710.5),
 libacl1 (= 2.3.1-1),
 libapache-pom-java (= 18-1),
 libarchive-zip-perl (= 1.68-1),
 libargtable2-0 (= 13-1.1),
 libasan6 (= 11.2.0-9+rpi1),
 libatomic1 (= 11.2.0-9+rpi1),
 libattr1 (= 1:2.5.1-1),
 libaudit-common (= 1:3.0.5-1),
 libaudit1 (= 1:3.0.5-1),
 libavahi-client3 (= 0.8-5),
 libavahi-common-data (= 0.8-5),
 libavahi-common3 (= 0.8-5),
 libbinutils (= 2.37-5+rpi1),
 libblas3 (= 3.10.0-1),
 libblkid1 (= 2.37.2-1),
 libboost-iostreams1.74.0 (= 1.74.0-9),
 libboost-program-options1.74.0 (= 1.74.0-9),
 libbrotli1 (= 1.0.9-2+b1),
 libbsd0 (= 0.11.3-1),
 libbz2-1.0 (= 1.0.8-4),
 libc-bin (= 2.32-4+rpi1),
 libc-dev-bin (= 2.32-4+rpi1),
 libc6 (= 2.32-4+rpi1),
 libc6-dev (= 2.32-4+rpi1),
 libcairo2 (= 1.16.0-5),
 libcap-ng0 (= 0.7.9-2.2+b1),
 libcc1-0 (= 11.2.0-9+rpi1),
 libcifpp1 (= 1.0.1-3),
 libcom-err2 (= 1.46.4-1),
 libcommons-logging-java (= 1.2-2),
 libcommons-parent-java (= 43-1),
 libcrypt-dev (= 1:4.4.25-2),
 libcrypt1 (= 1:4.4.25-2),
 libctf-nobfd0 (= 2.37-5+rpi1),
 libctf0 (= 2.37-5+rpi1),
 libcups2 (= 2.3.3op2-7),
 libcurl3-gnutls (= 7.74.0-1.3),
 libdb5.3 (= 5.3.28+dfsg1-0.8),
 libdbus-1-3 (= 1.12.20-2),
 libdebconfclient0 (= 0.260),
 libdebhelper-perl (= 13.5.2),
 libdeflate0 (= 1.8-1),
 libdpkg-perl (= 1.20.9+rpi1),
 libelf1 (= 0.185-2),
 libexpat1 (= 2.4.1-2),
 libexpat1-dev (= 2.4.1-2),
 libffi7 (= 3.3-6),
 libffi8 (= 3.4.2-3),
 libfile-stripnondeterminism-perl (= 1.12.0-2),
 libfontbox-java (= 1:1.8.16-2),
 libfontconfig1 (= 2.13.1-4.2),
 libfreetype6 (= 2.11.0+dfsg-1),
 libfribidi0 (= 1.0.8-2),
 libgcc-10-dev (= 10.3.0-9+rpi1),
 libgcc-s1 (= 11.2.0-9+rpi1),
 libgcrypt20 (= 1.9.4-3),
 libgd3 (= 2.3.0-2),
 libgdbm-compat4 (= 1.21-1),
 libgdbm6 (= 1.21-1),
 libgfortran5 (= 11.2.0-9+rpi1),
 libglib2.0-0 (= 2.70.0-1),
 libgmp10 (= 2:6.2.1+dfsg-2),
 libgnutls30 (= 3.7.2-2),
 libgomp1 (= 11.2.0-9+rpi1),
 libgpg-error0 (= 1.42-3),
 libgraphite2-3 (= 1.3.14-1),
 libgs9 (= 9.54.0~dfsg-5),
 libgs9-common (= 9.54.0~dfsg-5),
 libgssapi-krb5-2 (= 1.18.3-7),
 libharfbuzz0b (= 2.7.4-1),
 libhogweed6 (= 3.7.3-1),
 libhpdf-2.3.0 (= 2.3.0+dfsg-1),
 libhts3 (= 1.13+ds-2),
 libhtscodecs2 (= 1.1.1-3),
 libice6 (= 2:1.0.10-1),
 libicu67 (= 67.1-7),
 libidn12 (= 1.38-3),
 libidn2-0 (= 2.3.2-2),
 libijs-0.35 (= 0.35-15),
 libimagequant0 (= 2.12.2-1.1),
 libisl23 (= 0.23-1),
 libjbig0 (= 2.1-3.1+b2),
 libjbig2dec0 (= 0.19-3),
 libjpeg62-turbo (= 1:2.0.6-4),
 libjs-jquery (= 3.5.1+dfsg+~3.5.5-7),
 libjs-jquery-ui (= 1.12.1+dfsg-8),
 libjs-sphinxdoc (= 4.2.0-4),
 libjs-underscore (= 1.9.1~dfsg-4),
 libk5crypto3 (= 1.18.3-7),
 libkeyutils1 (= 1.6.1-2),
 libkpathsea6 (= 2021.20210626.59705-1),
 libkrb5-3 (= 1.18.3-7),
 libkrb5support0 (= 1.18.3-7),
 liblapack3 (= 3.10.0-1),
 liblbfgsb0 (= 3.0+dfsg.3-9),
 liblcms2-2 (= 2.12~rc1-2),
 libldap-2.4-2 (= 2.4.59+dfsg-1),
 liblmdb0 (= 0.9.24-1),
 liblz4-1 (= 1.9.3-2),
 liblzma5 (= 5.2.5-2),
 libmagic-mgc (= 1:5.39-3),
 libmagic1 (= 1:5.39-3),
 libmariadb3 (= 1:10.5.12-1),
 libmbedcrypto3 (= 2.16.9-0.1),
 libmbedtls12 (= 2.16.9-0.1),
 libmbedx509-0 (= 2.16.9-0.1),
 libmd0 (= 1.0.4-1),
 libmount1 (= 2.37.2-1),
 libmpc3 (= 1.2.0-1),
 libmpdec3 (= 2.5.1-2+rpi1),
 libmpfr6 (= 4.1.0-3),
 libncurses6 (= 6.2+20201114-4),
 libncursesw6 (= 6.2+20201114-4),
 libnetpbm10 (= 2:10.0-15.4),
 libnettle8 (= 3.7.3-1),
 libnghttp2-14 (= 1.43.0-1),
 libnsl-dev (= 1.3.0-2),
 libnsl2 (= 1.3.0-2),
 libopenjp2-7 (= 2.4.0-3),
 libp11-kit0 (= 0.24.0-2),
 libpam-modules (= 1.4.0-10),
 libpam-modules-bin (= 1.4.0-10),
 libpam-runtime (= 1.4.0-10),
 libpam0g (= 1.4.0-10),
 libpaper-utils (= 1.1.28),
 libpaper1 (= 1.1.28),
 libpcre2-8-0 (= 10.36-2),
 libpcre3 (= 2:8.39-13),
 libpdfbox-java (= 1:1.8.16-2),
 libperl5.32 (= 5.32.1-5),
 libpipeline1 (= 1.5.3-1),
 libpixman-1-0 (= 0.40.0-1),
 libpng16-16 (= 1.6.37-3),
 libpq5 (= 14.0-1),
 libpsl5 (= 0.21.0-1.2),
 libptexenc1 (= 2021.20210626.59705-1),
 libpython3-all-dev (= 3.9.2-3),
 libpython3-dev (= 3.9.2-3),
 libpython3-stdlib (= 3.9.2-3),
 libpython3.9 (= 3.9.7-4+rpi1),
 libpython3.9-dev (= 3.9.7-4+rpi1),
 libpython3.9-minimal (= 3.9.7-4+rpi1),
 libpython3.9-stdlib (= 3.9.7-4+rpi1),
 libraqm0 (= 0.7.0-4),
 libreadline8 (= 8.1-2),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
 libsasl2-2 (= 2.1.27+dfsg-2.1),
 libsasl2-modules-db (= 2.1.27+dfsg-2.1),
 libseccomp2 (= 2.5.1-1+rpi1),
 libselinux1 (= 3.1-3),
 libsigsegv2 (= 2.13-1),
 libsm6 (= 2:1.2.3-1),
 libsmartcols1 (= 2.37.2-1),
 libsqlite3-0 (= 3.36.0-2),
 libssh2-1 (= 1.10.0-2),
 libssl1.1 (= 1.1.1l-1),
 libstdc++-10-dev (= 10.3.0-9+rpi1),
 libstdc++6 (= 11.2.0-9+rpi1),
 libsub-override-perl (= 0.09-2),
 libsynctex2 (= 2021.20210626.59705-1),
 libsystemd0 (= 247.9-1+rpi1),
 libtasn1-6 (= 4.17.0-2),
 libteckit0 (= 2.5.10+ds1-3),
 libtexlua53 (= 2021.20210626.59705-1),
 libtexluajit2 (= 2021.20210626.59705-1),
 libtiff5 (= 4.3.0-2),
 libtinfo6 (= 6.2+20201114-4),
 libtirpc-common (= 1.3.2-2),
 libtirpc-dev (= 1.3.2-2),
 libtirpc3 (= 1.3.2-2),
 libtool (= 2.4.6-15),
 libubsan1 (= 11.2.0-9+rpi1),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 247.9-1+rpi1),
 libunistring2 (= 0.9.10-6),
 libuuid1 (= 2.37.2-1),
 libwebp6 (= 0.6.1-2.1),
 libwebpdemux2 (= 0.6.1-2.1),
 libwebpmux3 (= 0.6.1-2.1),
 libx11-6 (= 2:1.7.2-2),
 libx11-data (= 2:1.7.2-2),
 libxau6 (= 1:1.0.9-1),
 libxaw7 (= 2:1.0.13-1.1),
 libxcb-render0 (= 1.14-3),
 libxcb-shm0 (= 1.14-3),
 libxcb1 (= 1.14-3),
 libxdmcp6 (= 1:1.1.2-3),
 libxext6 (= 2:1.3.4-1),
 libxi6 (= 2:1.8-1),
 libxml2 (= 2.9.12+dfsg-5),
 libxmu6 (= 2:1.1.2-2+b3),
 libxpm4 (= 1:3.5.12-1),
 libxrender1 (= 1:0.9.10-1),
 libxt6 (= 1:1.2.0-1),
 libzstd1 (= 1.4.8+dfsg-2.1+rpi1),
 libzzip-0-13 (= 0.13.72+dfsg.1-1.1),
 linux-libc-dev (= 5.10.46-4+rpi1),
 login (= 1:4.8.1-1),
 lsb-base (= 11.1.0+rpi1),
 m4 (= 1.4.18-5),
 mafft (= 7.487-1),
 mailcap (= 3.70),
 make (= 4.3-4.1),
 man-db (= 2.9.4-2),
 mariadb-common (= 1:10.5.12-1),
 mawk (= 1.3.4.20200120-2),
 media-types (= 4.0.0),
 mime-support (= 3.66),
 muscle (= 1:3.8.1551-2),
 mysql-common (= 5.8+1.0.7),
 ncbi-blast+ (= 2.11.0+ds-1),
 ncbi-data (= 6.1.20170106+dfsg1-9),
 ncurses-base (= 6.2+20201114-4),
 ncurses-bin (= 6.2+20201114-4),
 netpbm (= 2:10.0-15.4),
 patch (= 2.7.6-7),
 perl (= 5.32.1-5),
 perl-base (= 5.32.1-5),
 perl-modules-5.32 (= 5.32.1-5),
 phylip (= 1:3.697+dfsg-2),
 po-debconf (= 1.0.21+nmu1),
 poppler-data (= 0.4.11-1),
 prank (= 0.0.170427+dfsg-3),
 preview-latex-style (= 12.2-1),
 probcons (= 1.12-14),
 python-matplotlib-data (= 3.3.4-2),
 python3 (= 3.9.2-3),
 python3-all (= 3.9.2-3),
 python3-all-dev (= 3.9.2-3),
 python3-cycler (= 0.10.0-3),
 python3-dateutil (= 2.8.1-6),
 python3-decorator (= 4.4.2-2),
 python3-dev (= 3.9.2-3),
 python3-distutils (= 3.9.7-1),
 python3-isodate (= 0.6.0-2),
 python3-kiwisolver (= 1.3.2-1),
 python3-lib2to3 (= 3.9.7-1),
 python3-linecache2 (= 1.0.0-4),
 python3-matplotlib (= 3.3.4-2),
 python3-minimal (= 3.9.2-3),
 python3-mmtf (= 1.1.2-3),
 python3-msgpack (= 1.0.2-2),
 python3-mysqldb (= 1.4.4-2+b1),
 python3-networkx (= 2.5+ds-2),
 python3-numpy (= 1:1.19.5-1),
 python3-pil (= 8.3.2-1),
 python3-pkg-resources (= 58.2.0-1),
 python3-psycopg2 (= 2.8.6-2),
 python3-pygments (= 2.7.1+dfsg-2.1),
 python3-pyparsing (= 2.4.7-1),
 python3-rdflib (= 5.0.0-1.1),
 python3-renderpm (= 3.5.59-2),
 python3-reportlab (= 3.5.59-2),
 python3-reportlab-accel (= 3.5.59-2),
 python3-scipy (= 1.6.0-2),
 python3-setuptools (= 58.2.0-1),
 python3-six (= 1.16.0-2),
 python3-traceback2 (= 1.4.0-6),
 python3-unittest2 (= 1.1.0-7),
 python3.9 (= 3.9.7-4+rpi1),
 python3.9-dev (= 3.9.7-4+rpi1),
 python3.9-minimal (= 3.9.7-4+rpi1),
 readline-common (= 8.1-2),
 rpcsvc-proto (= 1.4.2-4),
 samtools (= 1.13-2),
 sed (= 4.8-1),
 sensible-utils (= 0.0.17),
 sysvinit-utils (= 3.00-1),
 t-coffee (= 13.41.0.28bdc39+dfsg-4),
 t1utils (= 1.41-4),
 tar (= 1.34+dfsg-1),
 tex-common (= 6.17),
 texlive-base (= 2021.20210921-1),
 texlive-binaries (= 2021.20210626.59705-1),
 texlive-fonts-recommended (= 2021.20210921-1),
 texlive-latex-base (= 2021.20210921-1),
 texlive-latex-extra (= 2021.20210921-1),
 texlive-latex-recommended (= 2021.20210921-1),
 texlive-pictures (= 2021.20210921-1),
 ttf-bitstream-vera (= 1.10-8.1),
 tzdata (= 2021a-1),
 ucf (= 3.0043),
 util-linux (= 2.37.2-1),
 wise (= 2.4.1-23),
 wise-data (= 2.4.1-23),
 x11-common (= 1:7.7+23),
 xdg-utils (= 1.1.3-4.1),
 xz-utils (= 5.2.5-2),
 zlib1g (= 1:1.2.11.dfsg-2),
 zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1634919048"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


python3-biopython-dbgsym_1.79+dfsg-1_armhf.deb
----------------------------------------------

 new Debian package, version 2.0.
 size 260228 bytes: control archive=956 bytes.
     704 bytes,    12 lines      control              
     945 bytes,     9 lines      md5sums              
 Package: python3-biopython-dbgsym
 Source: python-biopython
 Version: 1.79+dfsg-1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 326
 Depends: python3-biopython (= 1.79+dfsg-1)
 Section: debug
 Priority: optional
 Description: debug symbols for python3-biopython
 Build-Ids: 447830dcb41bc93e852eeabe27a76ead035663bd 51c438816490ec44864785e74b0f178a5a2d5d17 7ee0a89918240eab79deb8b814f7f5bd52b41855 7f43ff03f4263fa2ac69efed2b206a9d5e4c477b 80859cc4fb508b2b287cc52f228c83a8e8324909 9d14e3e423364b7ebeb5729e1afff5fd1af21882 b4d4bccc0d9f2ef168ad149e2101d70c4c60155e d2e8988139082ab0a00c6c562ddceaca6e161b80

drwxr-xr-x root/root         0 2021-10-22 16:10 ./
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/44/
-rw-r--r-- root/root      9996 2021-10-22 16:10 ./usr/lib/debug/.build-id/44/7830dcb41bc93e852eeabe27a76ead035663bd.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/51/
-rw-r--r-- root/root      7468 2021-10-22 16:10 ./usr/lib/debug/.build-id/51/c438816490ec44864785e74b0f178a5a2d5d17.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/7e/
-rw-r--r-- root/root    138108 2021-10-22 16:10 ./usr/lib/debug/.build-id/7e/e0a89918240eab79deb8b814f7f5bd52b41855.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/7f/
-rw-r--r-- root/root     30200 2021-10-22 16:10 ./usr/lib/debug/.build-id/7f/43ff03f4263fa2ac69efed2b206a9d5e4c477b.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/80/
-rw-r--r-- root/root      9596 2021-10-22 16:10 ./usr/lib/debug/.build-id/80/859cc4fb508b2b287cc52f228c83a8e8324909.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/9d/
-rw-r--r-- root/root     88420 2021-10-22 16:10 ./usr/lib/debug/.build-id/9d/14e3e423364b7ebeb5729e1afff5fd1af21882.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/b4/
-rw-r--r-- root/root     14416 2021-10-22 16:10 ./usr/lib/debug/.build-id/b4/d4bccc0d9f2ef168ad149e2101d70c4c60155e.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.build-id/d2/
-rw-r--r-- root/root      6088 2021-10-22 16:10 ./usr/lib/debug/.build-id/d2/e8988139082ab0a00c6c562ddceaca6e161b80.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root      5604 2021-10-22 16:10 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-biopython.debug
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/share/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/share/doc/
lrwxrwxrwx root/root         0 2021-10-22 16:10 ./usr/share/doc/python3-biopython-dbgsym -> python3-biopython


python3-biopython_1.79+dfsg-1_armhf.deb
---------------------------------------

 new Debian package, version 2.0.
 size 1400316 bytes: control archive=16400 bytes.
    1492 bytes,    26 lines      control              
   57770 bytes,   613 lines      md5sums              
     271 bytes,    12 lines   *  postinst             #!/bin/sh
     420 bytes,    12 lines   *  prerm                #!/bin/sh
 Package: python3-biopython
 Source: python-biopython
 Version: 1.79+dfsg-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 9247
 Depends: python3-numpy (>= 1:1.16.0~rc1), python3-numpy-abi9, python3 (<< 3.10), python3 (>= 3.9~), python3:any, libc6 (>= 2.4), python3-renderpm, python3-reportlab
 Recommends: python-biopython-doc (= 1.79+dfsg-1), ncbi-blast+ (>= 2.10.1-3)
 Suggests: python3-tk, bwa, clustalo, clustalw, dialign, dssp (>= 4.0.0), emboss, fasttree, mafft, muscle, phylip, phyml, prank, probcons, python3-mysqldb, python3-matplotlib, python3-mmtf, python3-pil, python3-rdflib, python3-psycopg2, python3-scipy, raxml, samtools, t-coffee, wise, w3-dtd-mathml
 Breaks: cnvkit (<< 0.9.7-1~), 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 2021-10-22 16:10 ./
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Affy/
-rw-r--r-- root/root     19568 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Affy/CelFile.py
-rw-r--r-- root/root       296 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Affy/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Align/
-rw-r--r-- root/root     22457 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/AlignInfo.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Align/Applications/
-rw-r--r-- root/root     10012 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_ClustalOmega.py
-rw-r--r-- root/root     20228 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Clustalw.py
-rw-r--r-- root/root     10101 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Dialign.py
-rw-r--r-- root/root      3444 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_MSAProbs.py
-rw-r--r-- root/root     19884 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Mafft.py
-rw-r--r-- root/root     35418 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Muscle.py
-rw-r--r-- root/root     10544 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Prank.py
-rw-r--r-- root/root      5238 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_Probcons.py
-rw-r--r-- root/root      4588 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/_TCoffee.py
-rw-r--r-- root/root      1193 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/Applications/__init__.py
-rw-r--r-- root/root     85572 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/__init__.py
-rw-r--r-- root/root    236030 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/_aligners.c
-rw-r--r-- root/root    123244 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-39-arm-linux-gnueabihf.so
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/
-rw-r--r-- root/root     17605 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/
-rw-r--r-- root/root      2387 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22
-rw-r--r-- root/root      2387 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6
-rw-r--r-- root/root      2387 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74
-rw-r--r-- root/root      2122 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45
-rw-r--r-- root/root      2122 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50
-rw-r--r-- root/root      2122 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62
-rw-r--r-- root/root      2124 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80
-rw-r--r-- root/root      2122 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90
-rw-r--r-- root/root      2451 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF
-rw-r--r-- root/root      1120 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG
-rw-r--r-- root/root      2380 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC
-rw-r--r-- root/root      2351 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992
-rw-r--r-- root/root       275 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70
-rw-r--r-- root/root      2818 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON
-rw-r--r-- root/root      2413 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES
-rw-r--r-- root/root      1542 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN
-rw-r--r-- root/root      1092 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN
-rw-r--r-- root/root      2859 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78
-rw-r--r-- root/root      1171 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4
-rw-r--r-- root/root      2068 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250
-rw-r--r-- root/root      2666 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30
-rw-r--r-- root/root      2666 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70
-rw-r--r-- root/root      1581 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO
-rw-r--r-- root/root      2456 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER
-rw-r--r-- root/root     25459 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER
-rw-r--r-- root/root      1543 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR
-rw-r--r-- root/root       402 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/AlignIO/
-rw-r--r-- root/root     12069 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/ClustalIO.py
-rw-r--r-- root/root      8748 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/EmbossIO.py
-rw-r--r-- root/root     13357 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/FastaIO.py
-rw-r--r-- root/root      5624 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/Interfaces.py
-rw-r--r-- root/root     33936 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/MafIO.py
-rw-r--r-- root/root     13403 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/MauveIO.py
-rw-r--r-- root/root     14180 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/MsfIO.py
-rw-r--r-- root/root      6024 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/NexusIO.py
-rw-r--r-- root/root     17145 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/PhylipIO.py
-rw-r--r-- root/root     26639 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/StockholmIO.py
-rw-r--r-- root/root     18757 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/AlignIO/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Alphabet/
-rw-r--r-- root/root      1200 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Alphabet/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Application/
-rw-r--r-- root/root     32132 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Application/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Blast/
-rw-r--r-- root/root     67019 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Blast/Applications.py
-rw-r--r-- root/root     13271 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Blast/NCBIWWW.py
-rw-r--r-- root/root     33453 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py
-rw-r--r-- root/root      3929 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Blast/ParseBlastTable.py
-rw-r--r-- root/root     15857 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Blast/Record.py
-rw-r--r-- root/root       350 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Blast/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/CAPS/
-rw-r--r-- root/root      4041 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/CAPS/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Cluster/
-rw-r--r-- root/root     50805 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Cluster/__init__.py
-rw-r--r-- root/root     87140 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Cluster/_cluster.cpython-39-arm-linux-gnueabihf.so
-rw-r--r-- root/root    169203 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Cluster/cluster.c
-rw-r--r-- root/root      4135 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Cluster/cluster.h
-rw-r--r-- root/root     77865 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Cluster/clustermodule.c
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Compass/
-rw-r--r-- root/root      6964 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Compass/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Data/
-rw-r--r-- root/root     50385 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Data/CodonTable.py
-rw-r--r-- root/root      9248 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Data/IUPACData.py
-rw-r--r-- root/root     17337 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Data/SCOPData.py
-rw-r--r-- root/root       353 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Data/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Emboss/
-rw-r--r-- root/root     49091 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Emboss/Applications.py
-rw-r--r-- root/root      5593 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Emboss/Primer3.py
-rw-r--r-- root/root      2529 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Emboss/PrimerSearch.py
-rw-r--r-- root/root       355 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Emboss/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Entrez/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/
-rw-r--r-- root/root       660 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_0.dtd
-rw-r--r-- root/root     33675 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd
-rw-r--r-- root/root       660 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_1.dtd
-rw-r--r-- root/root     33691 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd
-rw-r--r-- root/root       660 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_2.dtd
-rw-r--r-- root/root     36007 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd
-rw-r--r-- root/root       660 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_3.dtd
-rw-r--r-- root/root     41304 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd
-rw-r--r-- root/root       660 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_4.dtd
-rw-r--r-- root/root     41537 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd
-rw-r--r-- root/root       792 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/EMBL_General.dtd
-rw-r--r-- root/root      2871 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/EMBL_General.mod.dtd
-rw-r--r-- root/root       807 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/GenBank_General.dtd
-rw-r--r-- root/root      1743 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/GenBank_General.mod.dtd
-rw-r--r-- root/root      3500 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/HomoloGene.dtd
-rw-r--r-- root/root      6460 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/HomoloGene.mod.dtd
-rw-r--r-- root/root       671 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/INSD_INSDSeq.dtd
-rw-r--r-- root/root     14705 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd
-rw-r--r-- root/root      3893 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB.dtd
-rw-r--r-- root/root      9382 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB.mod.dtd
-rw-r--r-- root/root      3908 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd
-rw-r--r-- root/root     17213 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd
-rw-r--r-- root/root      3902 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Features.dtd
-rw-r--r-- root/root     28680 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Features.mod.dtd
-rw-r--r-- root/root      3910 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Structural_model.dtd
-rw-r--r-- root/root     25075 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd
-rw-r--r-- root/root       665 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Access.dtd
-rw-r--r-- root/root      1221 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Access.mod.dtd
-rw-r--r-- root/root       785 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Biblio.dtd
-rw-r--r-- root/root     15918 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd
-rw-r--r-- root/root       925 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioSource.dtd
-rw-r--r-- root/root      4641 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd
-rw-r--r-- root/root       671 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioTree.dtd
-rw-r--r-- root/root      2444 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd
-rw-r--r-- root/root      3740 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Blast4.dtd
-rw-r--r-- root/root     39597 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd
-rw-r--r-- root/root      3507 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastDL.dtd
-rw-r--r-- root/root      4281 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd
-rw-r--r-- root/root       692 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd
-rw-r--r-- root/root      6579 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd
-rw-r--r-- root/root      4347 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cdd.dtd
-rw-r--r-- root/root     28292 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd
-rw-r--r-- root/root      4005 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cn3d.dtd
-rw-r--r-- root/root     16758 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd
-rw-r--r-- root/root       410 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd
-rw-r--r-- root/root       671 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrez2.dtd
-rw-r--r-- root/root     21922 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd
-rw-r--r-- root/root      3525 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd
-rw-r--r-- root/root     10316 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd
-rw-r--r-- root/root       671 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_FeatDef.dtd
-rw-r--r-- root/root      2358 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd
-rw-r--r-- root/root       659 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_GBSeq.dtd
-rw-r--r-- root/root     11502 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd
-rw-r--r-- root/root       776 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Gene.dtd
-rw-r--r-- root/root      2381 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd
-rw-r--r-- root/root       671 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_General.dtd
-rw-r--r-- root/root      8215 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_General.mod.dtd
-rw-r--r-- root/root      3629 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID1Access.dtd
-rw-r--r-- root/root      5733 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd
-rw-r--r-- root/root      3757 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID2Access.dtd
-rw-r--r-- root/root     23205 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd
-rw-r--r-- root/root      1378 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_MedArchive.dtd
-rw-r--r-- root/root      6931 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd
-rw-r--r-- root/root       907 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medlars.dtd
-rw-r--r-- root/root      1617 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd
-rw-r--r-- root/root       907 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medline.dtd
-rw-r--r-- root/root      5757 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd
-rw-r--r-- root/root       647 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mim.dtd
-rw-r--r-- root/root      8395 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd
-rw-r--r-- root/root      4461 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mime.dtd
-rw-r--r-- root/root      7270 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd
-rw-r--r-- root/root       665 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd
-rw-r--r-- root/root      3131 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd
-rw-r--r-- root/root       796 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Organism.dtd
-rw-r--r-- root/root      5250 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd
-rw-r--r-- root/root      1519 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCAssay.dtd
-rw-r--r-- root/root     31800 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd
-rw-r--r-- root/root      1155 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd
-rw-r--r-- root/root     43623 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd
-rw-r--r-- root/root      3736 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Project.dtd
-rw-r--r-- root/root      3769 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Project.mod.dtd
-rw-r--r-- root/root       791 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Protein.dtd
-rw-r--r-- root/root      1791 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd
-rw-r--r-- root/root      1003 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Pub.dtd
-rw-r--r-- root/root      2700 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd
-rw-r--r-- root/root      1021 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PubMed.dtd
-rw-r--r-- root/root      1698 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd
-rw-r--r-- root/root      3383 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_RNA.dtd
-rw-r--r-- root/root      3379 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd
-rw-r--r-- root/root      3495 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Remap.dtd
-rw-r--r-- root/root      4064 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd
-rw-r--r-- root/root       781 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Rsite.dtd
-rw-r--r-- root/root      1044 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd
-rw-r--r-- root/root      3629 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd
-rw-r--r-- root/root     19503 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd
-rw-r--r-- root/root       671 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqCode.dtd
-rw-r--r-- root/root      4231 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd
-rw-r--r-- root/root      3389 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqTable.dtd
-rw-r--r-- root/root      9912 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd
-rw-r--r-- root/root      3634 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seq_split.dtd
-rw-r--r-- root/root     11475 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd
-rw-r--r-- root/root      3389 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqalign.dtd
-rw-r--r-- root/root     15026 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd
-rw-r--r-- root/root      3387 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd
-rw-r--r-- root/root     19204 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd
-rw-r--r-- root/root      3385 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqloc.dtd
-rw-r--r-- root/root      7383 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd
-rw-r--r-- root/root      3385 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqres.dtd
-rw-r--r-- root/root      3149 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd
-rw-r--r-- root/root      3501 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqset.dtd
-rw-r--r-- root/root      3479 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd
-rw-r--r-- root/root      3384 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Sequence.dtd
-rw-r--r-- root/root     26293 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd
-rw-r--r-- root/root      3617 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Submit.dtd
-rw-r--r-- root/root      4130 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd
-rw-r--r-- root/root      3379 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Systems.dtd
-rw-r--r-- root/root       656 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TSeq.dtd
-rw-r--r-- root/root      1660 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd
-rw-r--r-- root/root      1138 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TxInit.dtd
-rw-r--r-- root/root      4625 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd
-rw-r--r-- root/root      3389 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Variation.dtd
-rw-r--r-- root/root     27155 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd
-rw-r--r-- root/root      7893 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NCBI_all.dtd
-rw-r--r-- root/root       625 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NSE.dtd
-rw-r--r-- root/root     26853 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/NSE.mod.dtd
-rw-r--r-- root/root      3470 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/OMSSA.dtd
-rw-r--r-- root/root     34917 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/OMSSA.mod.dtd
-rw-r--r-- root/root       787 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PDB_General.dtd
-rw-r--r-- root/root      1815 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PDB_General.mod.dtd
-rw-r--r-- root/root      3387 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PIR_General.dtd
-rw-r--r-- root/root      2076 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PIR_General.mod.dtd
-rw-r--r-- root/root       667 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PRF_General.dtd
-rw-r--r-- root/root      1535 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/PRF_General.mod.dtd
-rw-r--r-- root/root      3386 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/SP_General.dtd
-rw-r--r-- root/root      2375 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/SP_General.mod.dtd
-rw-r--r-- root/root     17329 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/XHTMLtablesetup.ent
-rw-r--r-- root/root     51298 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivearticle.dtd
-rw-r--r-- root/root      8304 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-classes.ent
-rw-r--r-- root/root     16646 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-mixes.ent
-rw-r--r-- root/root     38921 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-models.ent
-rw-r--r-- root/root      6412 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/archivecustom-modules.ent
-rw-r--r-- root/root     98004 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/articlemeta.ent
-rw-r--r-- root/root     15090 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/backmatter.ent
-rw-r--r-- root/root      2645 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_100301.dtd
-rw-r--r-- root/root      2645 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_110101.dtd
-rw-r--r-- root/root      2645 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_120101.dtd
-rw-r--r-- root/root      2756 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_130101.dtd
-rw-r--r-- root/root      2756 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_140101.dtd
-rw-r--r-- root/root      2756 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/bookdoc_150101.dtd
-rw-r--r-- root/root     21412 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/chars.ent
-rw-r--r-- root/root    152388 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/common.ent
-rw-r--r-- root/root     33182 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/default-classes.ent
-rw-r--r-- root/root     19402 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/default-mixes.ent
-rw-r--r-- root/root     82067 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/display.ent
-rw-r--r-- root/root      1655 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eInfo_020511.dtd
-rw-r--r-- root/root      2299 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eLink_090910.dtd
-rw-r--r-- root/root      2447 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eLink_101123.dtd
-rw-r--r-- root/root       520 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/ePost_020511.dtd
-rw-r--r-- root/root      2392 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSearch_020511.dtd
-rw-r--r-- root/root       736 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSpell.dtd
-rw-r--r-- root/root       602 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/eSummary_041029.dtd
-rw-r--r-- root/root       851 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/egquery.dtd
-rw-r--r-- root/root      1715 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/einfo.dtd
-rw-r--r-- root/root       466 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/elink_020122.dtd
-rw-r--r-- root/root      3337 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/esearch.dtd
-rw-r--r-- root/root       602 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/esummary-v1.dtd
-rw-r--r-- root/root     22746 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/format.ent
-rw-r--r-- root/root      9849 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/htmltable.dtd
-rw-r--r-- root/root     11589 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsa.ent
-rw-r--r-- root/root      9556 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsb.ent
-rw-r--r-- root/root      2254 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsc.ent
-rw-r--r-- root/root      7945 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsn.ent
-rw-r--r-- root/root      4432 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamso.ent
-rw-r--r-- root/root     14133 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isoamsr.ent
-rw-r--r-- root/root      3507 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isobox.ent
-rw-r--r-- root/root      5257 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isocyr1.ent
-rw-r--r-- root/root      2457 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isocyr2.ent
-rw-r--r-- root/root      1473 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isodia.ent
-rw-r--r-- root/root      4102 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk1.ent
-rw-r--r-- root/root      2389 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk2.ent
-rw-r--r-- root/root      3699 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk3.ent
-rw-r--r-- root/root      3591 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isogrk4.ent
-rw-r--r-- root/root      5199 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isolat1.ent
-rw-r--r-- root/root      8865 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isolat2.ent
-rw-r--r-- root/root      4478 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomfrk.ent
-rw-r--r-- root/root      2522 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomopf.ent
-rw-r--r-- root/root      4557 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isomscr.ent
-rw-r--r-- root/root      5816 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isonum.ent
-rw-r--r-- root/root      6594 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isopub.ent
-rw-r--r-- root/root     12399 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/isotech.ent
-rw-r--r-- root/root     18988 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/journalmeta.ent
-rw-r--r-- root/root     28360 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/link.ent
-rw-r--r-- root/root     25663 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/list.ent
-rw-r--r-- root/root     18334 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/math.ent
-rw-r--r-- root/root      6820 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml-in-pubmed.mod
lrwxrwxrwx root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd -> ../../../../../../share/xml/schema/w3c/mathml/dtd/mathml2.dtd
-rw-r--r-- root/root     12255 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml3-qname1.mod
-rw-r--r-- root/root     42407 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml3.dtd
-rw-r--r-- root/root     10452 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathmlsetup.ent
-rw-r--r-- root/root     37695 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mmlalias.ent
-rw-r--r-- root/root      7776 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mmlextra.ent
-rw-r--r-- root/root     21313 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/modules.ent
-rw-r--r-- root/root      4465 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd
-rw-r--r-- root/root     12369 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd
-rw-r--r-- root/root      5839 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_011101.dtd
-rw-r--r-- root/root      7946 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_080101.dtd
-rw-r--r-- root/root      8638 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmcommon_090101.dtd
-rw-r--r-- root/root      2053 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_011101.dtd
-rw-r--r-- root/root      3017 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_080101.dtd
-rw-r--r-- root/root      3195 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedline_090101.dtd
-rw-r--r-- root/root      6760 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd
-rw-r--r-- root/root      5001 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd
-rw-r--r-- root/root      5262 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd
-rw-r--r-- root/root      9322 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd
-rw-r--r-- root/root      9618 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd
-rw-r--r-- root/root      9308 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd
-rw-r--r-- root/root      8829 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd
-rw-r--r-- root/root      8995 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd
-rw-r--r-- root/root      9033 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd
-rw-r--r-- root/root      9112 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd
-rw-r--r-- root/root      8947 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd
-rw-r--r-- root/root      5672 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmserials_080101.dtd
-rw-r--r-- root/root      6703 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmserials_100101.dtd
-rw-r--r-- root/root      3185 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd
-rw-r--r-- root/root      3317 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd
-rw-r--r-- root/root      9656 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/notat.ent
-rw-r--r-- root/root     23807 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/para.ent
-rw-r--r-- root/root     15750 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/phrase.ent
-rw-r--r-- root/root     25142 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pmc-1.dtd
-rw-r--r-- root/root      2714 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_020114.dtd
-rw-r--r-- root/root      3045 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_080101.dtd
-rw-r--r-- root/root      3059 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_090101.dtd
-rw-r--r-- root/root      3126 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_100101.dtd
-rw-r--r-- root/root      3434 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_100301.dtd
-rw-r--r-- root/root      3434 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_110101.dtd
-rw-r--r-- root/root      3434 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_120101.dtd
-rw-r--r-- root/root      3434 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_130101.dtd
-rw-r--r-- root/root      3445 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_130501.dtd
-rw-r--r-- root/root      3445 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_140101.dtd
-rw-r--r-- root/root      3445 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_150101.dtd
-rw-r--r-- root/root     13062 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_180101.dtd
-rw-r--r-- root/root     13869 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_180601.dtd
-rw-r--r-- root/root     14576 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/pubmed_190101.dtd
-rw-r--r-- root/root     40015 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/references.ent
-rw-r--r-- root/root     13173 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/section.ent
-rw-r--r-- root/root      4003 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/taxon.dtd
-rw-r--r-- root/root     13595 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/DTDs/xmlspecchars.ent
-rw-r--r-- root/root     40328 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/Parser.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Entrez/XSDs/
-rw-r--r-- root/root      3536 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/XSDs/IPGReportSet.xsd
-rw-r--r-- root/root     26288 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Entrez/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/ExPASy/
-rw-r--r-- root/root      4455 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/ExPASy/Enzyme.py
-rw-r--r-- root/root      5015 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/ExPASy/Prodoc.py
-rw-r--r-- root/root     11665 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/ExPASy/Prosite.py
-rw-r--r-- root/root      4865 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/ExPASy/ScanProsite.py
-rw-r--r-- root/root      4110 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/ExPASy/__init__.py
-rw-r--r-- root/root      5598 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/ExPASy/cellosaurus.py
-rw-r--r-- root/root     24009 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/File.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/GenBank/
-rw-r--r-- root/root     23306 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/GenBank/Record.py
-rw-r--r-- root/root     86102 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/GenBank/Scanner.py
-rw-r--r-- root/root     64599 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/GenBank/__init__.py
-rw-r--r-- root/root      2271 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/GenBank/utils.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Geo/
-rw-r--r-- root/root      3067 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Geo/Record.py
-rw-r--r-- root/root      2176 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Geo/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Graphics/
-rw-r--r-- root/root     31451 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/BasicChromosome.py
-rw-r--r-- root/root      7365 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/ColorSpiral.py
-rw-r--r-- root/root      6472 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py
-rw-r--r-- root/root      6860 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/DisplayRepresentation.py
-rw-r--r-- root/root      9377 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/
-rw-r--r-- root/root     18533 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py
-rw-r--r-- root/root     68565 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py
-rw-r--r-- root/root      9678 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Colors.py
-rw-r--r-- root/root      3309 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py
-rw-r--r-- root/root     15639 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Diagram.py
-rw-r--r-- root/root      8059 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Feature.py
-rw-r--r-- root/root      7812 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py
-rw-r--r-- root/root      6945 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Graph.py
-rw-r--r-- root/root      5650 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py
-rw-r--r-- root/root     63242 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py
-rw-r--r-- root/root     11679 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/_Track.py
-rw-r--r-- root/root      1172 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/GenomeDiagram/__init__.py
-rw-r--r-- root/root     17646 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/KGML_vis.py
-rw-r--r-- root/root      3234 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Graphics/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/HMM/
-rw-r--r-- root/root     12526 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/HMM/DynamicProgramming.py
-rw-r--r-- root/root     26602 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/HMM/MarkovModel.py
-rw-r--r-- root/root     16574 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/HMM/Trainer.py
-rw-r--r-- root/root      2176 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/HMM/Utilities.py
-rw-r--r-- root/root       283 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/HMM/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/KEGG/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/KEGG/Compound/
-rw-r--r-- root/root      5319 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/Compound/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/KEGG/Enzyme/
-rw-r--r-- root/root     10930 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/Enzyme/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/KEGG/Gene/
-rw-r--r-- root/root      4216 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/Gene/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/
-rw-r--r-- root/root      6197 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/KGML_parser.py
-rw-r--r-- root/root     27698 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/KGML_pathway.py
-rw-r--r-- root/root       516 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/KGML/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/KEGG/Map/
-rw-r--r-- root/root      1642 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/Map/__init__.py
-rw-r--r-- root/root     10968 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/REST.py
-rw-r--r-- root/root      3027 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/KEGG/__init__.py
-rw-r--r-- root/root      4307 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/LogisticRegression.py
-rw-r--r-- root/root     23661 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/MarkovModel.py
-rw-r--r-- root/root     10888 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/MaxEntropy.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Medline/
-rw-r--r-- root/root      5913 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Medline/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/NMR/
-rw-r--r-- root/root      3353 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/NMR/NOEtools.py
-rw-r--r-- root/root       332 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/NMR/__init__.py
-rw-r--r-- root/root      9275 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/NMR/xpktools.py
-rw-r--r-- root/root      7962 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/NaiveBayes.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Nexus/
-rw-r--r-- root/root     84576 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py
-rw-r--r-- root/root      5745 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Nexus/Nodes.py
-rw-r--r-- root/root      4006 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Nexus/StandardData.py
-rw-r--r-- root/root     39979 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Nexus/Trees.py
-rw-r--r-- root/root       388 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Nexus/__init__.py
-rw-r--r-- root/root      3736 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Nexus/cnexus.c
-rw-r--r-- root/root      5604 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Nexus/cnexus.cpython-39-arm-linux-gnueabihf.so
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/PDB/
-rw-r--r-- root/root      4083 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/AbstractPropertyMap.py
-rw-r--r-- root/root     18343 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Atom.py
-rw-r--r-- root/root      6663 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Chain.py
-rw-r--r-- root/root     20535 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/PDB/DSSP.py
-rw-r--r-- root/root      2321 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Dice.py
-rw-r--r-- root/root     15258 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Entity.py
-rw-r--r-- root/root      9626 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/FragmentMapper.py
-rw-r--r-- root/root     11327 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/HSExposure.py
-rw-r--r-- root/root      4883 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/MMCIF2Dict.py
-rw-r--r-- root/root     21234 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/MMCIFParser.py
-rw-r--r-- root/root      2205 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Model.py
-rw-r--r-- root/root      7182 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/NACCESS.py
-rw-r--r-- root/root      4423 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/NeighborSearch.py
-rw-r--r-- root/root       762 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/PDBExceptions.py
-rw-r--r-- root/root     13309 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/PDBIO.py
-rw-r--r-- root/root     21840 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/PDBList.py
-rw-r--r-- root/root     17450 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py
-rw-r--r-- root/root     15502 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/PICIO.py
-rw-r--r-- root/root      3030 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/PSEA.py
-rw-r--r-- root/root     13987 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Polypeptide.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/
-rw-r--r-- root/root      5359 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/__init__.py
-rw-r--r-- root/root      9125 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.c
-rw-r--r-- root/root      9700 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-39-arm-linux-gnueabihf.so
-rw-r--r-- root/root      5268 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Residue.py
-rw-r--r-- root/root     21854 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/ResidueDepth.py
-rw-r--r-- root/root      8333 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/SASA.py
-rw-r--r-- root/root     31907 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/SCADIO.py
-rw-r--r-- root/root      2528 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Selection.py
-rw-r--r-- root/root      2079 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Structure.py
-rw-r--r-- root/root      3182 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/StructureAlignment.py
-rw-r--r-- root/root     11708 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py
-rw-r--r-- root/root      1947 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/Superimposer.py
-rw-r--r-- root/root      2478 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/__init__.py
-rw-r--r-- root/root     15603 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/ic_data.py
-rw-r--r-- root/root     13034 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/ic_rebuild.py
-rw-r--r-- root/root    129910 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/internal_coords.py
-rw-r--r-- root/root     42796 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/kdtrees.c
-rw-r--r-- root/root     18912 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/PDB/kdtrees.cpython-39-arm-linux-gnueabihf.so
-rw-r--r-- root/root     15410 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/mmcifio.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/
-rw-r--r-- root/root      8949 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/DefaultParser.py
-rw-r--r-- root/root      1546 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/__init__.py
-rw-r--r-- root/root     10167 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/mmtf/mmtfio.py
-rw-r--r-- root/root     11664 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/parse_pdb_header.py
-rw-r--r-- root/root     18339 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PDB/vectors.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Pathway/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/
-rw-r--r-- root/root      5869 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/Graph.py
-rw-r--r-- root/root      6783 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/MultiGraph.py
-rw-r--r-- root/root       575 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Pathway/Rep/__init__.py
-rw-r--r-- root/root     10763 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Pathway/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Phylo/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/
-rw-r--r-- root/root     27404 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Fasttree.py
-rw-r--r-- root/root     10846 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Phyml.py
-rw-r--r-- root/root     18860 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/_Raxml.py
-rw-r--r-- root/root       751 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/Applications/__init__.py
-rw-r--r-- root/root     45412 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/BaseTree.py
-rw-r--r-- root/root      1662 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/CDAO.py
-rw-r--r-- root/root     16106 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py
-rw-r--r-- root/root     23544 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/Consensus.py
-rw-r--r-- root/root      1403 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/NeXML.py
-rw-r--r-- root/root     11338 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/NeXMLIO.py
-rw-r--r-- root/root      1298 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/Newick.py
-rw-r--r-- root/root     12490 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/NewickIO.py
-rw-r--r-- root/root      2652 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/NexusIO.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/
-rw-r--r-- root/root       325 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/__init__.py
-rw-r--r-- root/root      5151 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_paml.py
-rw-r--r-- root/root     11409 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_baseml.py
-rw-r--r-- root/root     21155 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_codeml.py
-rw-r--r-- root/root      6820 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/_parse_yn00.py
-rw-r--r-- root/root      8320 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/baseml.py
-rw-r--r-- root/root      3727 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/chi2.py
-rw-r--r-- root/root      8878 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/codeml.py
-rw-r--r-- root/root      5743 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PAML/yn00.py
-rw-r--r-- root/root     50552 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py
-rw-r--r-- root/root     32759 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py
-rw-r--r-- root/root     43060 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/TreeConstruction.py
-rw-r--r-- root/root       513 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/__init__.py
-rw-r--r-- root/root    109270 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/_cdao_owl.py
-rw-r--r-- root/root      2595 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/_io.py
-rw-r--r-- root/root     17911 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Phylo/_utils.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/PopGen/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/
-rw-r--r-- root/root     34313 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/Controller.py
-rw-r--r-- root/root      7719 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/EasyController.py
-rw-r--r-- root/root     11790 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/FileParser.py
-rw-r--r-- root/root      3849 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/LargeFileParser.py
-rw-r--r-- root/root      7461 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PopGen/GenePop/__init__.py
-rw-r--r-- root/root       359 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/PopGen/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Restriction/
-rw-r--r-- root/root     16234 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Restriction/PrintFormat.py
-rw-r--r-- root/root     85637 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Restriction/Restriction.py
-rw-r--r-- root/root    439594 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Restriction/Restriction_Dictionary.py
-rw-r--r-- root/root      7856 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Restriction/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SCOP/
-rw-r--r-- root/root      3924 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SCOP/Cla.py
-rw-r--r-- root/root      3006 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SCOP/Des.py
-rw-r--r-- root/root      2467 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SCOP/Dom.py
-rw-r--r-- root/root      2966 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SCOP/Hie.py
-rw-r--r-- root/root     10304 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SCOP/Raf.py
-rw-r--r-- root/root      3063 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SCOP/Residues.py
-rw-r--r-- root/root     32785 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SCOP/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SVDSuperimposer/
-rw-r--r-- root/root      6210 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SVDSuperimposer/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SearchIO/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/
-rw-r--r-- root/root     23896 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/__init__.py
-rw-r--r-- root/root     33766 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_tab.py
-rw-r--r-- root/root      5610 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_text.py
-rw-r--r-- root/root     37110 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlastIO/blast_xml.py
-rw-r--r-- root/root     31231 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/BlatIO.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/
-rw-r--r-- root/root     12965 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/__init__.py
-rw-r--r-- root/root     19992 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/_base.py
-rw-r--r-- root/root      4089 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py
-rw-r--r-- root/root     20436 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py
-rw-r--r-- root/root      8244 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py
-rw-r--r-- root/root     25908 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/FastaIO.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/
-rw-r--r-- root/root       639 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/__init__.py
-rw-r--r-- root/root      9309 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/
-rw-r--r-- root/root     20309 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/__init__.py
-rw-r--r-- root/root      1482 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/_base.py
-rw-r--r-- root/root     12839 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py
-rw-r--r-- root/root     13956 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py
-rw-r--r-- root/root     12818 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py
-rw-r--r-- root/root     18733 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/
-rw-r--r-- root/root      5155 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/__init__.py
-rw-r--r-- root/root      7455 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py
-rw-r--r-- root/root     29010 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/__init__.py
-rw-r--r-- root/root      1213 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_index.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/
-rw-r--r-- root/root     75041 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/NCBIStandalone.py
-rw-r--r-- root/root     12123 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/ParserSupport.py
-rw-r--r-- root/root       313 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_legacy/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/
-rw-r--r-- root/root      2464 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/__init__.py
-rw-r--r-- root/root      2650 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/_base.py
-rw-r--r-- root/root     17356 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/hit.py
-rw-r--r-- root/root     48189 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/hsp.py
-rw-r--r-- root/root     30434 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_model/query.py
-rw-r--r-- root/root      5597 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SearchIO/_utils.py
-rw-r--r-- root/root    111899 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Seq.py
-rw-r--r-- root/root     76081 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqFeature.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SeqIO/
-rw-r--r-- root/root     26098 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/AbiIO.py
-rw-r--r-- root/root      4091 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/AceIO.py
-rw-r--r-- root/root     15000 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/FastaIO.py
-rw-r--r-- root/root      8071 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/GckIO.py
-rw-r--r-- root/root      4433 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/IgIO.py
-rw-r--r-- root/root     57359 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py
-rw-r--r-- root/root     14029 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/Interfaces.py
-rw-r--r-- root/root      5843 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/NibIO.py
-rw-r--r-- root/root     19768 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/PdbIO.py
-rw-r--r-- root/root      6075 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/PhdIO.py
-rw-r--r-- root/root     10304 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/PirIO.py
-rw-r--r-- root/root     90189 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/QualityIO.py
-rw-r--r-- root/root     27598 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/SeqXmlIO.py
-rw-r--r-- root/root     55779 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/SffIO.py
-rw-r--r-- root/root      9633 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/SnapGeneIO.py
-rw-r--r-- root/root      6001 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/SwissIO.py
-rw-r--r-- root/root      5020 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/TabIO.py
-rw-r--r-- root/root     10810 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py
-rw-r--r-- root/root     25529 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/UniprotIO.py
-rw-r--r-- root/root     12548 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/XdnaIO.py
-rw-r--r-- root/root     43749 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py
-rw-r--r-- root/root     27383 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqIO/_index.py
-rw-r--r-- root/root     21992 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.c
-rw-r--r-- root/root      9896 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SeqIO/_twoBitIO.cpython-39-arm-linux-gnueabihf.so
-rw-r--r-- root/root     54689 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqRecord.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SeqUtils/
-rw-r--r-- root/root      3513 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CheckSum.py
-rw-r--r-- root/root      6789 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CodonUsage.py
-rw-r--r-- root/root      1380 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/CodonUsageIndices.py
-rw-r--r-- root/root      6474 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/IsoelectricPoint.py
-rw-r--r-- root/root     45300 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/MeltingTemp.py
-rw-r--r-- root/root     13364 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/ProtParam.py
-rw-r--r-- root/root     18172 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/ProtParamData.py
-rw-r--r-- root/root     15035 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/__init__.py
-rw-r--r-- root/root      5755 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SeqUtils/lcc.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Sequencing/
-rw-r--r-- root/root     20711 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Sequencing/Ace.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/
-rw-r--r-- root/root      8588 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_Novoalign.py
-rw-r--r-- root/root      2189 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/__init__.py
-rw-r--r-- root/root     28256 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_bwa.py
-rw-r--r-- root/root     36658 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Sequencing/Applications/_samtools.py
-rw-r--r-- root/root      5598 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Sequencing/Phd.py
-rw-r--r-- root/root       530 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Sequencing/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SubsMat/
-rw-r--r-- root/root      2821 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SubsMat/FreqTable.py
-rw-r--r-- root/root    174096 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SubsMat/MatrixInfo.py
-rw-r--r-- root/root     20833 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SubsMat/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/SwissProt/
-rw-r--r-- root/root      3490 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SwissProt/KeyWList.py
-rw-r--r-- root/root     33077 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/SwissProt/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/TogoWS/
-rw-r--r-- root/root     13951 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/TogoWS/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/UniGene/
-rw-r--r-- root/root     12811 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/UniGene/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/UniProt/
-rw-r--r-- root/root     15076 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/UniProt/GOA.py
-rw-r--r-- root/root       722 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/UniProt/__init__.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/Wise/
-rw-r--r-- root/root      4701 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Wise/__init__.py
-rw-r--r-- root/root      4819 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Wise/dnal.py
-rw-r--r-- root/root      4608 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/Wise/psw.py
-rw-r--r-- root/root      4721 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/__init__.py
-rw-r--r-- root/root      2095 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/_utils.py
-rw-r--r-- root/root     37532 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/bgzf.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/codonalign/
-rw-r--r-- root/root     30019 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/codonalign/__init__.py
-rw-r--r-- root/root      3281 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/codonalign/chisq.py
-rw-r--r-- root/root     18027 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/codonalign/codonalignment.py
-rw-r--r-- root/root     47918 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/codonalign/codonseq.py
-rw-r--r-- root/root      9824 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-39-arm-linux-gnueabihf.so
-rw-r--r-- root/root     16043 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/cpairwise2module.c
-rw-r--r-- root/root      4295 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/kNN.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/motifs/
-rw-r--r-- root/root     20517 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/__init__.py
-rw-r--r-- root/root      5800 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/_pwm.c
-rw-r--r-- root/root      9936 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/motifs/_pwm.cpython-39-arm-linux-gnueabihf.so
-rw-r--r-- root/root      2107 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/alignace.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/motifs/applications/
-rw-r--r-- root/root       582 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/applications/__init__.py
-rw-r--r-- root/root     10382 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/applications/_xxmotif.py
-rw-r--r-- root/root      2528 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/clusterbuster.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/
-rw-r--r-- root/root     11315 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/__init__.py
-rw-r--r-- root/root     27729 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/jaspar/db.py
-rw-r--r-- root/root      4828 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/mast.py
-rw-r--r-- root/root     20515 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/matrix.py
-rw-r--r-- root/root      6716 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/meme.py
-rw-r--r-- root/root      5767 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/minimal.py
-rw-r--r-- root/root     16438 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/pfm.py
-rw-r--r-- root/root      4534 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/thresholds.py
-rw-r--r-- root/root     11915 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/transfac.py
-rw-r--r-- root/root      3843 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/motifs/xms.py
-rw-r--r-- root/root     52649 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/pairwise2.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/Bio/phenotype/
-rw-r--r-- root/root      8318 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/phenotype/__init__.py
-rw-r--r-- root/root     37672 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/phenotype/phen_micro.py
-rw-r--r-- root/root      4062 2021-06-01 07:11 ./usr/lib/python3/dist-packages/Bio/phenotype/pm_fitting.py
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/biopython-1.79.egg-info/
-rw-r--r-- root/root     12922 2021-10-22 16:10 ./usr/lib/python3/dist-packages/biopython-1.79.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2021-10-22 16:10 ./usr/lib/python3/dist-packages/biopython-1.79.egg-info/dependency_links.txt
-rw-r--r-- root/root         0 2021-10-22 16:10 ./usr/lib/python3/dist-packages/biopython-1.79.egg-info/requires.txt
-rw-r--r-- root/root        11 2021-10-22 16:10 ./usr/lib/python3/dist-packages/biopython-1.79.egg-info/top_level.txt
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/share/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/share/doc/python3-biopython/
-rw-r--r-- root/root      5072 2021-06-01 07:11 ./usr/share/doc/python3-biopython/CONTRIB.rst.gz
-rw-r--r-- root/root      1970 2021-06-01 07:11 ./usr/share/doc/python3-biopython/CONTRIBUTING.rst.gz
-rw-r--r-- root/root      9931 2021-06-01 07:11 ./usr/share/doc/python3-biopython/DEPRECATED.rst.gz
-rw-r--r-- root/root     36664 2021-06-01 07:11 ./usr/share/doc/python3-biopython/NEWS.rst.gz
-rw-r--r-- root/root       273 2021-08-22 17:54 ./usr/share/doc/python3-biopython/README.Debian
-rw-r--r-- root/root      7436 2021-10-22 16:10 ./usr/share/doc/python3-biopython/changelog.Debian.gz
-rw-r--r-- root/root      2055 2021-10-22 16:10 ./usr/share/doc/python3-biopython/copyright
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/share/lintian/
drwxr-xr-x root/root         0 2021-10-22 16:10 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       278 2021-08-22 17:54 ./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: 293644
Build-Time: 1604
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1646
Job: python-biopython_1.79+dfsg-1
Machine Architecture: armhf
Package: python-biopython
Package-Time: 3282
Source-Version: 1.79+dfsg-1
Space: 293644
Status: successful
Version: 1.79+dfsg-1
--------------------------------------------------------------------------------
Finished at 2021-10-25T07:35:23Z
Build needed 00:54:42, 293644k disk space