Raspbian Package Auto-Building

python-biopython → 1.80+dfsg-3 → armhf → 2022-12-26 12:17:55

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| python-biopython 1.80+dfsg-3 (armhf)         Mon, 26 Dec 2022 10:52:39 +0000 |
+==============================================================================+

Package: python-biopython
Version: 1.80+dfsg-3
Source Version: 1.80+dfsg-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-ea309678-1a4b-41bc-9694-866c6d3c673f' with '<<CHROOT>>'

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

Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.8 MB in 10s (2849 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'python-biopython' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-biopython.git
Please use:
git clone https://salsa.debian.org/med-team/python-biopython.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 10.7 MB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main python-biopython 1.80+dfsg-3 (dsc) [3404 B]
Get:2 http://172.17.4.1/private bookworm-staging/main python-biopython 1.80+dfsg-3 (tar) [10.7 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main python-biopython 1.80+dfsg-3 (diff) [19.9 kB]
Fetched 10.7 MB in 1s (9014 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-biopython-nfLYp1/python-biopython-1.80+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-biopython-nfLYp1' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


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

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-TKJI6k/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-TKJI6k/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-TKJI6k/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (8443 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  krb5-locales libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 13 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (67.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12958 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| 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, 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
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, 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
dpkg-deb: building package 'sbuild-build-depends-python-biopython-dummy' in '/<<BUILDDIR>>/resolver-TKJI6k/apt_archive/sbuild-build-depends-python-biopython-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-python-biopython-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ Sources [790 B]
Get:5 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ Packages [799 B]
Fetched 2922 B in 0s (13.0 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install python-biopython build dependencies (apt-based resolver)
----------------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev blt bsdextrautils bwa clustalo
  clustalw debhelper dh-autoreconf dh-python dh-strip-nondeterminism dialign
  dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config
  fonts-dejavu-core fonts-lmodern fonts-lyx fonts-urw-base35 gettext
  gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick
  imagemagick-6-common imagemagick-6.q16 intltool-debian libabsl20210324
  libaom3 libapache-pom-java libarchive-zip-perl libargtable2-0
  libavahi-client3 libavahi-common-data libavahi-common3 libavif15 libblas3
  libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-regex1.74.0
  libbrotli1 libbsd0 libcairo2 libcifpp-data libcifpp2 libcommons-logging-java
  libcommons-parent-java libcups2 libcurl3-gnutls libdav1d6 libdbus-1-3
  libde265-0 libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java
  libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgd3
  libgfortran5 libglib2.0-0 libgraphite2-3 libgs-common libgs10 libgs10-common
  libharfbuzz0b libheif1 libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu72
  libidn12 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg62-turbo
  libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6
  liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblmdb0 liblqr-1-0 libltdl7
  libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6
  libmariadb3 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmd0 libmpdec3
  libncurses6 libnetpbm11 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
  libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib
  libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
  libqhull-r8.0 libraqm0 librav1e0 librtmp1 libsm6 libssh2-1
  libsub-override-perl libsvtav1enc1 libsynctex2 libtcl8.6 libteckit0
  libtexlua53-5 libtexluajit2 libtiff5 libtk8.6 libtool libuchardet0 libwebp7
  libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx265-199 libxau6 libxaw7
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2
  libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6 libyuv0 libzzip-0-13
  m4 mafft mailcap man-db mariadb-common media-types mime-support mysql-common
  ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank
  preview-latex-style probcons python-matplotlib-data python3 python3-all
  python3-all-dev python3-appdirs python3-attr python3-brotli python3-cycler
  python3-dateutil python3-decorator python3-dev python3-distutils
  python3-fonttools python3-fs python3-isodate python3-kiwisolver
  python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal
  python3-mmtf python3-mpmath python3-msgpack python3-mysqldb python3-networkx
  python3-numpy python3-packaging python3-pil python3-pil.imagetk
  python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing
  python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel
  python3-scipy python3-setuptools python3-six python3-sympy python3-tk
  python3-tz python3-ufolib2 python3-unicodedata2 python3-unittest2 python3.10
  python3.10-dev python3.10-minimal python3.11 python3.11-dev
  python3.11-minimal samtools t-coffee t1utils tex-common texlive-base
  texlive-binaries texlive-fonts-recommended texlive-latex-base
  texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5
  ucf unicode-data wise wise-data x11-common xdg-utils xfonts-encodings
  xfonts-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc blt-demo clustalx seaview
  dh-make flit python3-build python3-tomli python3-installer emboss-doc
  emboss-test embassy bison flex-doc fonts-freefont-otf | fonts-freefont-ttf
  fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff hevea-doc
  imagemagick-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp
  gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance
  sane-utils transfig ufraw-batch libavalon-framework-java
  libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java
  cups-common libfftw3-bin libfftw3-dev libgd-tools low-memory-monitor
  libjs-jquery-ui-docs liblcms2-utils libmagickcore-6.q16-6-extra tcl8.6 tk8.6
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho
  | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic
  fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra python3-doc
  python3-venv python-attr-doc python-cycler-doc python-lxml-doc
  cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 inkscape ipython3
  librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi
  python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado
  texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server
  | virtual-mysql-server python-networkx-doc gfortran python-numpy-doc
  python3-pytest python-pil-doc python-psycopg2-doc python-pygments-doc
  ttf-bitstream-vera python-pyparsing-doc python-rdflib-doc pdf-viewer
  python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc
  python-setuptools-doc texlive-fonts-extra python-sympy-doc tix
  python3-tk-dbg python3.10-venv python3.10-doc binfmt-support python3.11-venv
  python3.11-doc cwltool boxshade t-coffee-examples perl-tk xpdf | pdf-viewer
  xzdec texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex
  icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science
  texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex
  texlive-pictures-doc vprerex wise-doc
Recommended packages:
  primer3 libfl-dev curl | wget | lynx libmagickcore-6.q16-6-extra
  ca-certificates dbus libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs fonts-droid-fallback javascript-common gsfonts libgpm2
  publicsuffix libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl
  python3-bs4 python3-html5lib python3-gdal python3-pydot python3-pygraphviz
  python3-yaml python3-olefile python3-sparqlwrapper isympy-common amap-align
  dialign-tx fsa kalign libsoap-lite-perl libxml-simple-perl muscle mustang
  poa proda tm-align lmodern dvisvgm tex-gyre tipa default-jre
  libspreadsheet-parseexcel-perl texlive-plain-generic tk
  libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
  x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev blt bsdextrautils bwa clustalo
  clustalw debhelper dh-autoreconf dh-python dh-strip-nondeterminism dialign
  dssp dwz emboss emboss-data emboss-lib fasttree file flex fontconfig-config
  fonts-dejavu-core fonts-lmodern fonts-lyx fonts-urw-base35 gettext
  gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick
  imagemagick-6-common imagemagick-6.q16 intltool-debian libabsl20210324
  libaom3 libapache-pom-java libarchive-zip-perl libargtable2-0
  libavahi-client3 libavahi-common-data libavahi-common3 libavif15 libblas3
  libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-regex1.74.0
  libbrotli1 libbsd0 libcairo2 libcifpp-data libcifpp2 libcommons-logging-java
  libcommons-parent-java libcups2 libcurl3-gnutls libdav1d6 libdbus-1-3
  libde265-0 libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java
  libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgd3
  libgfortran5 libglib2.0-0 libgraphite2-3 libgs-common libgs10 libgs10-common
  libharfbuzz0b libheif1 libhpdf-2.3.0 libhts3 libhtscodecs2 libice6 libicu72
  libidn12 libijs-0.35 libimagequant0 libjbig0 libjbig2dec0 libjpeg62-turbo
  libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libkpathsea6
  liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblmdb0 liblqr-1-0 libltdl7
  libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6
  libmariadb3 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmd0 libmpdec3
  libncurses6 libnetpbm11 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
  libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib
  libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
  libqhull-r8.0 libraqm0 librav1e0 librtmp1 libsm6 libssh2-1
  libsub-override-perl libsvtav1enc1 libsynctex2 libtcl8.6 libteckit0
  libtexlua53-5 libtexluajit2 libtiff5 libtk8.6 libtool libuchardet0 libwebp7
  libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx265-199 libxau6 libxaw7
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2
  libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6 libyuv0 libzzip-0-13
  m4 mafft mailcap man-db mariadb-common media-types mime-support mysql-common
  ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank
  preview-latex-style probcons python-matplotlib-data python3 python3-all
  python3-all-dev python3-appdirs python3-attr python3-brotli python3-cycler
  python3-dateutil python3-decorator python3-dev python3-distutils
  python3-fonttools python3-fs python3-isodate python3-kiwisolver
  python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal
  python3-mmtf python3-mpmath python3-msgpack python3-mysqldb python3-networkx
  python3-numpy python3-packaging python3-pil python3-pil.imagetk
  python3-pkg-resources python3-psycopg2 python3-pygments python3-pyparsing
  python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel
  python3-scipy python3-setuptools python3-six python3-sympy python3-tk
  python3-tz python3-ufolib2 python3-unicodedata2 python3-unittest2 python3.10
  python3.10-dev python3.10-minimal python3.11 python3.11-dev
  python3.11-minimal samtools sbuild-build-depends-python-biopython-dummy
  t-coffee t1utils tex-common texlive-base texlive-binaries
  texlive-fonts-recommended texlive-latex-base texlive-latex-extra
  texlive-latex-recommended texlive-pictures tk8.6-blt2.5 ucf unicode-data
  wise wise-data x11-common xdg-utils xfonts-encodings xfonts-utils zlib1g-dev
0 upgraded, 274 newly installed, 0 to remove and 13 not upgraded.
Need to get 307 MB of archives.
After this operation, 1513 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-TKJI6k/apt_archive ./ sbuild-build-depends-python-biopython-dummy 0.invalid.0 [1084 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf flex armhf 2.6.4-8.1 [411 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.39-2 [258 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libfontenc1 armhf 1:1.1.4-1 [22.3 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf xfonts-encodings all 1:1.0.4-2.1 [573 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf xfonts-utils armhf 1:7.7+6 [82.5 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf fonts-urw-base35 all 20200910-6 [6374 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libaom3 armhf 3.5.0-1 [1302 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libdav1d6 armhf 1.0.0-2+rpi1 [205 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libde265-0 armhf 1.0.9-1+rpi1 [186 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libx265-199 armhf 3.5-2 [548 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libheif1 armhf 1.13.0-1 [169 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-6.1 [27.0 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.13.1-1 [125 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.1-2 [1214 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.1 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-5 [390 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libopenjp2-7 armhf 2.5.0-1 [165 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-2 [133 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2+b1 [237 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.4.0-6 [278 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libwebpdemux2 armhf 1.2.2-2+b1 [95.5 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libwebpmux3 armhf 1.2.2-2+b1 [103 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf imagemagick-6-common all 8:6.9.11.60+dfsg-1.3 [211 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libmagickcore-6.q16-6 armhf 8:6.9.11.60+dfsg-1.3+b4 [1607 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libmagickwand-6.q16-6 armhf 8:6.9.11.60+dfsg-1.3+b4 [385 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf poppler-data all 0.4.11-1 [1608 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.9-1 [769 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.9-1 [1477 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-3 [25.5 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf mailcap all 3.70+nmu1 [32.0 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.9-1 [1597 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.9-1 [509 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-3 [8588 B]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-3 [25.2 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-minimal armhf 3.11.1-1 [797 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf python3.11-minimal armhf 3.11.1-1 [1679 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libtcl8.6 armhf 8.6.13+dfsg-1 [906 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.6-1 [53.7 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libtk8.6 armhf 8.6.13-1 [680 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-4.1 [477 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf blt armhf 2.5.3+dfsg-4.1 [14.9 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf bwa armhf 0.7.17-7 [196 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libargtable2-0 armhf 13-1.1 [15.9 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf clustalo armhf 1.2.4-7 [222 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf clustalw armhf 2.1+lgpl-7 [229 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.3 [81.1 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.3 [942 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.8-1 [77.3 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.8-1 [139 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf dialign armhf 2.2.1-11 [134 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-18 [235 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libboost-program-options1.74.0 armhf 1.74.0-18 [306 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-18 [420 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libcifpp-data all 2.0.5-4 [438 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libcifpp2 armhf 2.0.5-4+b1 [781 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf dssp armhf 4.0.4-1 [492 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libabsl20210324 armhf 0~20210324.2-4+rpi1 [331 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libgav1-1 armhf 0.18.0-1+rpi1 [272 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf librav1e0 armhf 0.5.1-5 [525 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libsvtav1enc1 armhf 1.4.1+dfsg-1 [880 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf libyuv0 armhf 0.0~git20221118.ea26d7a-2 [80.0 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libavif15 armhf 0.11.1-1 [84.1 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libxpm4 armhf 1:3.5.12-1 [43.6 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libgd3 armhf 2.3.3-7 [102 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libhpdf-2.3.0 armhf 2.3.0+dfsg-1 [330 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf mysql-common all 5.8+1.0.8 [7528 B]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf mariadb-common all 1:10.6.11-1 [20.7 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libmariadb3 armhf 1:10.6.11-1 [147 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libpq5 armhf 15.1-1 [164 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf emboss-lib armhf 6.6.0+dfsg-12 [2587 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf emboss-data all 6.6.0+dfsg-12 [61.1 MB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf emboss armhf 6.6.0+dfsg-12 [1021 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf fasttree armhf 2.1.11-2 [158 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf fonts-lmodern all 2.005-1 [4540 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf fonts-lyx all 2.3.6.1-1 [206 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libgs-common all 10.0.0~dfsg-9 [148 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf libgs10-common all 10.0.0~dfsg-9 [586 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common-data armhf 0.8-6+b1 [124 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common3 armhf 0.8-6+b1 [55.8 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libdbus-1-3 armhf 1.14.4-1 [211 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libavahi-client3 armhf 0.8-6+b1 [58.5 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf libcups2 armhf 2.4.2-1+b1 [311 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libidn12 armhf 1.41-1 [80.8 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libijs-0.35 armhf 0.35-15 [14.7 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libjbig2dec0 armhf 0.19-3+b2 [58.6 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libxt6 armhf 1:1.2.1-1 [159 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf libgs10 armhf 10.0.0~dfsg-9 [2050 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf ghostscript armhf 10.0.0~dfsg-9 [56.4 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf libnetpbm11 armhf 2:10.97.00-2 [164 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf netpbm armhf 2:10.97.00-2 [1807 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf tex-common all 6.18 [32.5 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf libkpathsea6 armhf 2022.20220321.62855-5 [142 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf libptexenc1 armhf 2022.20220321.62855-5 [40.1 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf libsynctex2 armhf 2022.20220321.62855-5 [46.3 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf libtexlua53-5 armhf 2022.20220321.62855-5 [81.3 kB]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf libtexluajit2 armhf 2022.20220321.62855-5 [187 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf t1utils armhf 1.41-4 [52.3 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.42.2-1 [461 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-7 [482 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 5.2.0-2+b1 [1832 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf libteckit0 armhf 2.5.11+ds1-1 [256 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf libxmu6 armhf 2:1.1.3-3 [52.0 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf libxaw7 armhf 2:1.0.14-1 [165 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf libxi6 armhf 2:1.8-1 [78.1 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf libzzip-0-13 armhf 0.13.72+dfsg.1-1.1 [54.3 kB]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf texlive-binaries armhf 2022.20220321.62855-5 [7474 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf texlive-base all 2022.20221123-1 [21.9 MB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf imagemagick-6.q16 armhf 8:6.9.11.60+dfsg-1.3+b4 [339 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf imagemagick armhf 8:6.9.11.60+dfsg-1.3+b4 [121 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf hevea armhf 2.36-1+b3 [1687 kB]
Get:173 http://172.17.4.1/private bookworm-staging/main armhf libapache-pom-java all 25-2 [5260 B]
Get:174 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:175 http://172.17.4.1/private bookworm-staging/main armhf libcommons-parent-java all 43-1 [10.8 kB]
Get:176 http://172.17.4.1/private bookworm-staging/main armhf libcommons-logging-java all 1.2-3 [62.4 kB]
Get:177 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.51.0-1 [60.5 kB]
Get:178 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:179 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:180 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:181 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.86.0-2 [318 kB]
Get:182 http://172.17.4.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.5.0-1 [130 kB]
Get:183 http://172.17.4.1/private bookworm-staging/main armhf libfontbox-java all 1:1.8.16-2 [211 kB]
Get:184 http://172.17.4.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2.1 [63.7 kB]
Get:185 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-10+rpi1 [238 kB]
Get:186 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-4 [59.5 kB]
Get:187 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-3 [367 kB]
Get:188 http://172.17.4.1/private bookworm-staging/main armhf libimagequant0 armhf 2.17.0-1 [28.0 kB]
Get:189 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:190 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:191 http://172.17.4.1/private bookworm-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-2 [116 kB]
Get:192 http://172.17.4.1/private bookworm-staging/main armhf libjs-sphinxdoc all 5.3.0-2 [130 kB]
Get:193 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:194 http://172.17.4.1/private bookworm-staging/main armhf liblbfgsb0 armhf 3.0+dfsg.3-11 [24.3 kB]
Get:195 http://172.17.4.1/private bookworm-staging/main armhf liblmdb0 armhf 0.9.24-1 [38.7 kB]
Get:196 http://172.17.4.1/private bookworm-staging/main armhf libmbedcrypto7 armhf 2.28.1-1 [243 kB]
Get:197 http://172.17.4.1/private bookworm-staging/main armhf libmbedx509-1 armhf 2.28.1-1 [125 kB]
Get:198 http://172.17.4.1/private bookworm-staging/main armhf libmbedtls14 armhf 2.28.1-1 [157 kB]
Get:199 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:200 http://172.17.4.1/private bookworm-staging/main armhf libpdfbox-java all 1:1.8.16-2 [5205 kB]
Get:201 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10 armhf 3.10.9-1 [1462 kB]
Get:202 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [901 kB]
Get:203 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-dev armhf 3.10.9-1 [2926 kB]
Get:204 http://172.17.4.1/private bookworm-staging/main armhf libpython3-dev armhf 3.10.6-3 [8820 B]
Get:205 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-stdlib armhf 3.11.1-1 [1621 kB]
Get:206 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11 armhf 3.11.1-1 [1669 kB]
Get:207 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-dev armhf 3.11.1-1 [3372 kB]
Get:208 http://172.17.4.1/private bookworm-staging/main armhf libpython3-all-dev armhf 3.10.6-3 [1072 B]
Get:209 http://172.17.4.1/private bookworm-staging/main armhf libqhull-r8.0 armhf 2020.2-5 [221 kB]
Get:210 http://172.17.4.1/private bookworm-staging/main armhf libraqm0 armhf 0.7.0-4 [9388 B]
Get:211 http://172.17.4.1/private bookworm-staging/main armhf libxslt1.1 armhf 1.1.35-1 [221 kB]
Get:212 http://172.17.4.1/private bookworm-staging/main armhf mafft armhf 7.505-1 [734 kB]
Get:213 http://172.17.4.1/private bookworm-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB]
Get:214 http://172.17.4.1/private bookworm-staging/main armhf ncbi-blast+ armhf 2.12.0+ds-3+b2 [9948 kB]
Get:215 http://172.17.4.1/private bookworm-staging/main armhf phylip armhf 1:3.697+dfsg-2 [683 kB]
Get:216 http://172.17.4.1/private bookworm-staging/main armhf prank armhf 0.0.170427+dfsg-3 [298 kB]
Get:217 http://172.17.4.1/private bookworm-staging/main armhf preview-latex-style all 12.2-1 [201 kB]
Get:218 http://172.17.4.1/private bookworm-staging/main armhf probcons armhf 1.12-14 [100 kB]
Get:219 http://172.17.4.1/private bookworm-staging/main armhf python-matplotlib-data all 3.5.2-4 [2725 kB]
Get:220 http://172.17.4.1/private bookworm-staging/main armhf python3.11 armhf 3.11.1-1 [567 kB]
Get:221 http://172.17.4.1/private bookworm-staging/main armhf python3-all armhf 3.10.6-3 [1064 B]
Get:222 http://172.17.4.1/private bookworm-staging/main armhf python3.10-dev armhf 3.10.9-1 [512 kB]
Get:223 http://172.17.4.1/private bookworm-staging/main armhf python3-dev armhf 3.10.6-3 [26.0 kB]
Get:224 http://172.17.4.1/private bookworm-staging/main armhf python3.11-dev armhf 3.11.1-1 [618 kB]
Get:225 http://172.17.4.1/private bookworm-staging/main armhf python3-all-dev armhf 3.10.6-3 [1076 B]
Get:226 http://172.17.4.1/private bookworm-staging/main armhf python3-appdirs all 1.4.4-3 [13.0 kB]
Get:227 http://172.17.4.1/private bookworm-staging/main armhf python3-attr all 22.2.0-1 [65.4 kB]
Get:228 http://172.17.4.1/private bookworm-staging/main armhf python3-brotli armhf 1.0.9-2+b2 [278 kB]
Get:229 http://172.17.4.1/private bookworm-staging/main armhf python3-cycler all 0.11.0-1 [8020 B]
Get:230 http://172.17.4.1/private bookworm-staging/main armhf python3-six all 1.16.0-4 [17.5 kB]
Get:231 http://172.17.4.1/private bookworm-staging/main armhf python3-dateutil all 2.8.2-1 [78.2 kB]
Get:232 http://172.17.4.1/private bookworm-staging/main armhf python3-decorator all 5.1.1-3 [14.9 kB]
Get:233 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 65.5.0-1 [278 kB]
Get:234 http://172.17.4.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.23.5-2+b1 [5285 kB]
Get:235 http://172.17.4.1/private bookworm-staging/main armhf python3-scipy armhf 1.8.1-14+rpi1 [12.9 MB]
Get:236 http://172.17.4.1/private bookworm-staging/main armhf python3-ufolib2 all 0.13.1+dfsg1-1 [32.0 kB]
Get:237 http://172.17.4.1/private bookworm-staging/main armhf python3-mpmath all 1.2.1-2 [418 kB]
Get:238 http://172.17.4.1/private bookworm-staging/main armhf python3-sympy all 1.11.1-1 [4358 kB]
Get:239 http://172.17.4.1/private bookworm-staging/main armhf python3-tz all 2022.6-1 [31.8 kB]
Get:240 http://172.17.4.1/private bookworm-staging/main armhf python3-fs all 2.4.16-2 [95.2 kB]
Get:241 http://172.17.4.1/private bookworm-staging/main armhf python3-lxml armhf 4.9.1-1 [959 kB]
Get:242 http://172.17.4.1/private bookworm-staging/main armhf python3-lz4 armhf 4.0.2+dfsg-1 [23.9 kB]
Get:243 http://172.17.4.1/private bookworm-staging/main armhf python3-unicodedata2 armhf 14.0.0+ds2-1 [298 kB]
Get:244 http://172.17.4.1/private bookworm-staging/main armhf unicode-data all 15.0.0-1 [7984 kB]
Get:245 http://172.17.4.1/private bookworm-staging/main armhf python3-fonttools armhf 4.37.4-1 [983 kB]
Get:246 http://172.17.4.1/private bookworm-staging/main armhf python3-isodate all 0.6.1-1 [25.3 kB]
Get:247 http://172.17.4.1/private bookworm-staging/main armhf python3-kiwisolver armhf 1.3.2-1+b1 [52.1 kB]
Get:248 http://172.17.4.1/private bookworm-staging/main armhf python3-pil armhf 9.2.0-1.1 [427 kB]
Get:249 http://172.17.4.1/private bookworm-staging/main armhf python3-tk armhf 3.10.8-1 [101 kB]
Get:250 http://172.17.4.1/private bookworm-staging/main armhf python3-pil.imagetk armhf 9.2.0-1.1 [71.8 kB]
Get:251 http://172.17.4.1/private bookworm-staging/main armhf python3-pyparsing all 3.0.9-1 [138 kB]
Get:252 http://172.17.4.1/private bookworm-staging/main armhf python3-packaging all 21.3-1.1 [34.2 kB]
Get:253 http://172.17.4.1/private bookworm-staging/main armhf python3-matplotlib armhf 3.5.2-4 [6479 kB]
Get:254 http://172.17.4.1/private bookworm-staging/main armhf python3-msgpack armhf 1.0.3-2 [62.1 kB]
Get:255 http://172.17.4.1/private bookworm-staging/main armhf python3-mmtf all 1.1.3-1 [17.0 kB]
Get:256 http://172.17.4.1/private bookworm-staging/main armhf python3-mysqldb armhf 1.4.6-2 [46.5 kB]
Get:257 http://172.17.4.1/private bookworm-staging/main armhf python3-networkx all 2.6.3-1 [943 kB]
Get:258 http://172.17.4.1/private bookworm-staging/main armhf python3-psycopg2 armhf 2.9.4-2 [108 kB]
Get:259 http://172.17.4.1/private bookworm-staging/main armhf python3-pygments all 2.13.0+dfsg-1 [767 kB]
Get:260 http://172.17.4.1/private bookworm-staging/main armhf python3-rdflib all 6.1.1-1 [385 kB]
Get:261 http://172.17.4.1/private bookworm-staging/main armhf python3-renderpm armhf 3.6.11-1 [69.9 kB]
Get:262 http://172.17.4.1/private bookworm-staging/main armhf python3-reportlab-accel armhf 3.6.11-1 [41.3 kB]
Get:263 http://172.17.4.1/private bookworm-staging/main armhf python3-reportlab all 3.6.11-1 [566 kB]
Get:264 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 65.5.0-1 [519 kB]
Get:265 http://172.17.4.1/private bookworm-staging/main armhf python3-unittest2 all 1.1.0-9 [75.8 kB]
Get:266 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.16.1-1 [559 kB]
Get:267 http://172.17.4.1/private bookworm-staging/main armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [786 kB]
Get:268 http://172.17.4.1/private bookworm-staging/main armhf texlive-fonts-recommended all 2022.20221123-1 [4988 kB]
Get:269 http://172.17.4.1/private bookworm-staging/main armhf texlive-latex-base all 2022.20221123-1 [1175 kB]
Get:270 http://172.17.4.1/private bookworm-staging/main armhf texlive-latex-recommended all 2022.20221123-1 [8882 kB]
Get:271 http://172.17.4.1/private bookworm-staging/main armhf texlive-pictures all 2022.20221123-1 [15.8 MB]
Get:272 http://172.17.4.1/private bookworm-staging/main armhf texlive-latex-extra all 2022.20221123-2 [19.2 MB]
Get:273 http://172.17.4.1/private bookworm-staging/main armhf wise-data all 2.4.1-23 [78.2 kB]
Get:274 http://172.17.4.1/private bookworm-staging/main armhf wise armhf 2.4.1-23 [704 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 307 MB in 32s (9609 kB/s)
Selecting previously unselected package m4.
(Reading database ... 12958 files and directories currently installed.)
Preparing to unpack .../00-m4_1.4.19-1_armhf.deb ...
Unpacking m4 (1.4.19-1) ...
Selecting previously unselected package flex.
Preparing to unpack .../01-flex_2.6.4-8.1_armhf.deb ...
Unpacking flex (2.6.4-8.1) ...
Selecting previously unselected package libfftw3-double3:armhf.
Preparing to unpack .../02-libfftw3-double3_3.3.10-1_armhf.deb ...
Unpacking libfftw3-double3:armhf (3.3.10-1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../03-libexpat1_2.5.0-1_armhf.deb ...
Unpacking libexpat1:armhf (2.5.0-1) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../04-libbrotli1_1.0.9-2+b2_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b2) ...
Selecting previously unselected package libpng16-16:armhf.
Preparing to unpack .../05-libpng16-16_1.6.39-2_armhf.deb ...
Unpacking libpng16-16:armhf (1.6.39-2) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../06-libfreetype6_2.12.1+dfsg-3_armhf.deb ...
Unpacking libfreetype6:armhf (2.12.1+dfsg-3) ...
Selecting previously unselected package ucf.
Preparing to unpack .../07-ucf_3.0043_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../08-fonts-dejavu-core_2.37-2_all.deb ...
Unpacking fonts-dejavu-core (2.37-2) ...
Selecting previously unselected package libfontenc1:armhf.
Preparing to unpack .../09-libfontenc1_1%3a1.1.4-1_armhf.deb ...
Unpacking libfontenc1:armhf (1:1.1.4-1) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../10-x11-common_1%3a7.7+23_all.deb ...
Unpacking x11-common (1:7.7+23) ...
Selecting previously unselected package xfonts-encodings.
Preparing to unpack .../11-xfonts-encodings_1%3a1.0.4-2.1_all.deb ...
Unpacking xfonts-encodings (1:1.0.4-2.1) ...
Selecting previously unselected package xfonts-utils.
Preparing to unpack .../12-xfonts-utils_1%3a7.7+6_armhf.deb ...
Unpacking xfonts-utils (1:7.7+6) ...
Selecting previously unselected package fonts-urw-base35.
Preparing to unpack .../13-fonts-urw-base35_20200910-6_all.deb ...
Unpacking fonts-urw-base35 (20200910-6) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../14-fontconfig-config_2.13.1-4.5_armhf.deb ...
Unpacking fontconfig-config (2.13.1-4.5) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../15-libfontconfig1_2.13.1-4.5_armhf.deb ...
Unpacking libfontconfig1:armhf (2.13.1-4.5) ...
Selecting previously unselected package libaom3:armhf.
Preparing to unpack .../16-libaom3_3.5.0-1_armhf.deb ...
Unpacking libaom3:armhf (3.5.0-1) ...
Selecting previously unselected package libdav1d6:armhf.
Preparing to unpack .../17-libdav1d6_1.0.0-2+rpi1_armhf.deb ...
Unpacking libdav1d6:armhf (1.0.0-2+rpi1) ...
Selecting previously unselected package libde265-0:armhf.
Preparing to unpack .../18-libde265-0_1.0.9-1+rpi1_armhf.deb ...
Unpacking libde265-0:armhf (1.0.9-1+rpi1) ...
Selecting previously unselected package libx265-199:armhf.
Preparing to unpack .../19-libx265-199_3.5-2_armhf.deb ...
Unpacking libx265-199:armhf (3.5-2) ...
Selecting previously unselected package libheif1:armhf.
Preparing to unpack .../20-libheif1_1.13.0-1_armhf.deb ...
Unpacking libheif1:armhf (1.13.0-1) ...
Selecting previously unselected package libjbig0:armhf.
Preparing to unpack .../21-libjbig0_2.1-6.1_armhf.deb ...
Unpacking libjbig0:armhf (2.1-6.1) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../22-libjpeg62-turbo_1%3a2.1.2-1_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.1.2-1) ...
Selecting previously unselected package liblcms2-2:armhf.
Preparing to unpack .../23-liblcms2-2_2.13.1-1_armhf.deb ...
Unpacking liblcms2-2:armhf (2.13.1-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../24-libglib2.0-0_2.74.1-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.74.1-2) ...
Selecting previously unselected package liblqr-1-0:armhf.
Preparing to unpack .../25-liblqr-1-0_0.4.2-2.1_armhf.deb ...
Unpacking liblqr-1-0:armhf (0.4.2-2.1) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../26-libltdl7_2.4.7-5_armhf.deb ...
Unpacking libltdl7:armhf (2.4.7-5) ...
Selecting previously unselected package libopenjp2-7:armhf.
Preparing to unpack .../27-libopenjp2-7_2.5.0-1_armhf.deb ...
Unpacking libopenjp2-7:armhf (2.5.0-1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../28-libdeflate0_1.14-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.14-1) ...
Selecting previously unselected package liblerc4:armhf.
Preparing to unpack .../29-liblerc4_4.0.0+ds-2_armhf.deb ...
Unpacking liblerc4:armhf (4.0.0+ds-2) ...
Selecting previously unselected package libwebp7:armhf.
Preparing to unpack .../30-libwebp7_1.2.2-2+b1_armhf.deb ...
Unpacking libwebp7:armhf (1.2.2-2+b1) ...
Selecting previously unselected package libtiff5:armhf.
Preparing to unpack .../31-libtiff5_4.4.0-6_armhf.deb ...
Unpacking libtiff5:armhf (4.4.0-6) ...
Selecting previously unselected package libwebpdemux2:armhf.
Preparing to unpack .../32-libwebpdemux2_1.2.2-2+b1_armhf.deb ...
Unpacking libwebpdemux2:armhf (1.2.2-2+b1) ...
Selecting previously unselected package libwebpmux3:armhf.
Preparing to unpack .../33-libwebpmux3_1.2.2-2+b1_armhf.deb ...
Unpacking libwebpmux3:armhf (1.2.2-2+b1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../34-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 .../35-libmd0_1.0.4-2_armhf.deb ...
Unpacking libmd0:armhf (1.0.4-2) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../36-libbsd0_0.11.7-1_armhf.deb ...
Unpacking libbsd0:armhf (0.11.7-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../37-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 .../38-libxcb1_1.15-1_armhf.deb ...
Unpacking libxcb1:armhf (1.15-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../39-libx11-data_2%3a1.8.1-2_all.deb ...
Unpacking libx11-data (2:1.8.1-2) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../40-libx11-6_2%3a1.8.1-2_armhf.deb ...
Unpacking libx11-6:armhf (2:1.8.1-2) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../41-libxext6_2%3a1.3.4-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.4-1) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../42-libicu72_72.1-3_armhf.deb ...
Unpacking libicu72:armhf (72.1-3) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../43-libxml2_2.9.14+dfsg-1.1_armhf.deb ...
Unpacking libxml2:armhf (2.9.14+dfsg-1.1) ...
Selecting previously unselected package imagemagick-6-common.
Preparing to unpack .../44-imagemagick-6-common_8%3a6.9.11.60+dfsg-1.3_all.deb ...
Unpacking imagemagick-6-common (8:6.9.11.60+dfsg-1.3) ...
Selecting previously unselected package libmagickcore-6.q16-6:armhf.
Preparing to unpack .../45-libmagickcore-6.q16-6_8%3a6.9.11.60+dfsg-1.3+b4_armhf.deb ...
Unpacking libmagickcore-6.q16-6:armhf (8:6.9.11.60+dfsg-1.3+b4) ...
Selecting previously unselected package libmagickwand-6.q16-6:armhf.
Preparing to unpack .../46-libmagickwand-6.q16-6_8%3a6.9.11.60+dfsg-1.3+b4_armhf.deb ...
Unpacking libmagickwand-6.q16-6:armhf (8:6.9.11.60+dfsg-1.3+b4) ...
Selecting previously unselected package poppler-data.
Preparing to unpack .../47-poppler-data_0.4.11-1_all.deb ...
Unpacking poppler-data (0.4.11-1) ...
Selecting previously unselected package libpython3.10-minimal:armhf.
Preparing to unpack .../48-libpython3.10-minimal_3.10.9-1_armhf.deb ...
Unpacking libpython3.10-minimal:armhf (3.10.9-1) ...
Selecting previously unselected package python3.10-minimal.
Preparing to unpack .../49-python3.10-minimal_3.10.9-1_armhf.deb ...
Unpacking python3.10-minimal (3.10.9-1) ...
Setting up libpython3.10-minimal:armhf (3.10.9-1) ...
Setting up libexpat1:armhf (2.5.0-1) ...
Setting up python3.10-minimal (3.10.9-1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 15252 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.10.6-3_armhf.deb ...
Unpacking python3-minimal (3.10.6-3) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_8.0.0_all.deb ...
Unpacking media-types (8.0.0) ...
Selecting previously unselected package mailcap.
Preparing to unpack .../2-mailcap_3.70+nmu1_all.deb ...
Unpacking mailcap (3.70+nmu1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../3-mime-support_3.66_all.deb ...
Unpacking mime-support (3.66) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../4-libmpdec3_2.5.1-2+rpi1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-2+rpi1) ...
Selecting previously unselected package libpython3.10-stdlib:armhf.
Preparing to unpack .../5-libpython3.10-stdlib_3.10.9-1_armhf.deb ...
Unpacking libpython3.10-stdlib:armhf (3.10.9-1) ...
Selecting previously unselected package python3.10.
Preparing to unpack .../6-python3.10_3.10.9-1_armhf.deb ...
Unpacking python3.10 (3.10.9-1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../7-libpython3-stdlib_3.10.6-3_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.10.6-3) ...
Setting up python3-minimal (3.10.6-3) ...
Selecting previously unselected package python3.
(Reading database ... 15678 files and directories currently installed.)
Preparing to unpack .../000-python3_3.10.6-3_armhf.deb ...
Unpacking python3 (3.10.6-3) ...
Selecting previously unselected package libpython3.11-minimal:armhf.
Preparing to unpack .../001-libpython3.11-minimal_3.11.1-1_armhf.deb ...
Unpacking libpython3.11-minimal:armhf (3.11.1-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../002-python3.11-minimal_3.11.1-1_armhf.deb ...
Unpacking python3.11-minimal (3.11.1-1) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../003-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../004-groff-base_1.22.4-9_armhf.deb ...
Unpacking groff-base (1.22.4-9) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../005-bsdextrautils_2.38.1-4_armhf.deb ...
Unpacking bsdextrautils (2.38.1-4) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../006-libpipeline1_1.5.7-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../007-man-db_2.11.1-1_armhf.deb ...
Unpacking man-db (2.11.1-1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../008-libmagic-mgc_1%3a5.41-4_armhf.deb ...
Unpacking libmagic-mgc (1:5.41-4) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../009-libmagic1_1%3a5.41-4_armhf.deb ...
Unpacking libmagic1:armhf (1:5.41-4) ...
Selecting previously unselected package file.
Preparing to unpack .../010-file_1%3a5.41-4_armhf.deb ...
Unpacking file (1:5.41-4) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../011-gettext-base_0.21-10_armhf.deb ...
Unpacking gettext-base (0.21-10) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../012-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../013-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../014-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../015-autopoint_0.21-10_all.deb ...
Unpacking autopoint (0.21-10) ...
Selecting previously unselected package libtcl8.6:armhf.
Preparing to unpack .../016-libtcl8.6_8.6.13+dfsg-1_armhf.deb ...
Unpacking libtcl8.6:armhf (8.6.13+dfsg-1) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../017-libxrender1_1%3a0.9.10-1.1_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1.1) ...
Selecting previously unselected package libxft2:armhf.
Preparing to unpack .../018-libxft2_2.3.6-1_armhf.deb ...
Unpacking libxft2:armhf (2.3.6-1) ...
Selecting previously unselected package libxss1:armhf.
Preparing to unpack .../019-libxss1_1%3a1.2.3-1_armhf.deb ...
Unpacking libxss1:armhf (1:1.2.3-1) ...
Selecting previously unselected package libtk8.6:armhf.
Preparing to unpack .../020-libtk8.6_8.6.13-1_armhf.deb ...
Unpacking libtk8.6:armhf (8.6.13-1) ...
Selecting previously unselected package tk8.6-blt2.5.
Preparing to unpack .../021-tk8.6-blt2.5_2.5.3+dfsg-4.1_armhf.deb ...
Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Selecting previously unselected package blt.
Preparing to unpack .../022-blt_2.5.3+dfsg-4.1_armhf.deb ...
Unpacking blt (2.5.3+dfsg-4.1) ...
Selecting previously unselected package bwa.
Preparing to unpack .../023-bwa_0.7.17-7_armhf.deb ...
Unpacking bwa (0.7.17-7) ...
Selecting previously unselected package libargtable2-0.
Preparing to unpack .../024-libargtable2-0_13-1.1_armhf.deb ...
Unpacking libargtable2-0 (13-1.1) ...
Selecting previously unselected package clustalo.
Preparing to unpack .../025-clustalo_1.2.4-7_armhf.deb ...
Unpacking clustalo (1.2.4-7) ...
Selecting previously unselected package clustalw.
Preparing to unpack .../026-clustalw_2.1+lgpl-7_armhf.deb ...
Unpacking clustalw (2.1+lgpl-7) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../027-libdebhelper-perl_13.11.3_all.deb ...
Unpacking libdebhelper-perl (13.11.3) ...
Selecting previously unselected package libtool.
Preparing to unpack .../028-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../029-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../030-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 .../031-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../032-libfile-stripnondeterminism-perl_1.13.0-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.0-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../033-dh-strip-nondeterminism_1.13.0-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.0-2) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../034-libelf1_0.187-2+rpi2_armhf.deb ...
Unpacking libelf1:armhf (0.187-2+rpi2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../035-dwz_0.14+20220924-2_armhf.deb ...
Unpacking dwz (0.14+20220924-2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../036-gettext_0.21-10_armhf.deb ...
Unpacking gettext (0.21-10) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../037-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../038-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../039-debhelper_13.11.3_all.deb ...
Unpacking debhelper (13.11.3) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../040-python3-lib2to3_3.10.8-1_all.deb ...
Unpacking python3-lib2to3 (3.10.8-1) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../041-python3-distutils_3.10.8-1_all.deb ...
Unpacking python3-distutils (3.10.8-1) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../042-dh-python_5.20220819+rpi1_all.deb ...
Unpacking dh-python (5.20220819+rpi1) ...
Selecting previously unselected package dialign.
Preparing to unpack .../043-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 .../044-libboost-iostreams1.74.0_1.74.0-18_armhf.deb ...
Unpacking libboost-iostreams1.74.0:armhf (1.74.0-18) ...
Selecting previously unselected package libboost-program-options1.74.0:armhf.
Preparing to unpack .../045-libboost-program-options1.74.0_1.74.0-18_armhf.deb ...
Unpacking libboost-program-options1.74.0:armhf (1.74.0-18) ...
Selecting previously unselected package libboost-regex1.74.0:armhf.
Preparing to unpack .../046-libboost-regex1.74.0_1.74.0-18_armhf.deb ...
Unpacking libboost-regex1.74.0:armhf (1.74.0-18) ...
Selecting previously unselected package libcifpp-data.
Preparing to unpack .../047-libcifpp-data_2.0.5-4_all.deb ...
Unpacking libcifpp-data (2.0.5-4) ...
Selecting previously unselected package libcifpp2:armhf.
Preparing to unpack .../048-libcifpp2_2.0.5-4+b1_armhf.deb ...
Unpacking libcifpp2:armhf (2.0.5-4+b1) ...
Selecting previously unselected package dssp.
Preparing to unpack .../049-dssp_4.0.4-1_armhf.deb ...
Unpacking dssp (4.0.4-1) ...
Selecting previously unselected package libabsl20210324:armhf.
Preparing to unpack .../050-libabsl20210324_0~20210324.2-4+rpi1_armhf.deb ...
Unpacking libabsl20210324:armhf (0~20210324.2-4+rpi1) ...
Selecting previously unselected package libgav1-1:armhf.
Preparing to unpack .../051-libgav1-1_0.18.0-1+rpi1_armhf.deb ...
Unpacking libgav1-1:armhf (0.18.0-1+rpi1) ...
Selecting previously unselected package librav1e0:armhf.
Preparing to unpack .../052-librav1e0_0.5.1-5_armhf.deb ...
Unpacking librav1e0:armhf (0.5.1-5) ...
Selecting previously unselected package libsvtav1enc1:armhf.
Preparing to unpack .../053-libsvtav1enc1_1.4.1+dfsg-1_armhf.deb ...
Unpacking libsvtav1enc1:armhf (1.4.1+dfsg-1) ...
Selecting previously unselected package libyuv0:armhf.
Preparing to unpack .../054-libyuv0_0.0~git20221118.ea26d7a-2_armhf.deb ...
Unpacking libyuv0:armhf (0.0~git20221118.ea26d7a-2) ...
Selecting previously unselected package libavif15:armhf.
Preparing to unpack .../055-libavif15_0.11.1-1_armhf.deb ...
Unpacking libavif15:armhf (0.11.1-1) ...
Selecting previously unselected package libxpm4:armhf.
Preparing to unpack .../056-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 .../057-libgd3_2.3.3-7_armhf.deb ...
Unpacking libgd3:armhf (2.3.3-7) ...
Selecting previously unselected package libhpdf-2.3.0:armhf.
Preparing to unpack .../058-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 .../059-mysql-common_5.8+1.0.8_all.deb ...
Unpacking mysql-common (5.8+1.0.8) ...
Selecting previously unselected package mariadb-common.
Preparing to unpack .../060-mariadb-common_1%3a10.6.11-1_all.deb ...
Unpacking mariadb-common (1:10.6.11-1) ...
Selecting previously unselected package libmariadb3:armhf.
Preparing to unpack .../061-libmariadb3_1%3a10.6.11-1_armhf.deb ...
Unpacking libmariadb3:armhf (1:10.6.11-1) ...
Selecting previously unselected package libpq5:armhf.
Preparing to unpack .../062-libpq5_15.1-1_armhf.deb ...
Unpacking libpq5:armhf (15.1-1) ...
Selecting previously unselected package emboss-lib.
Preparing to unpack .../063-emboss-lib_6.6.0+dfsg-12_armhf.deb ...
Unpacking emboss-lib (6.6.0+dfsg-12) ...
Selecting previously unselected package emboss-data.
Preparing to unpack .../064-emboss-data_6.6.0+dfsg-12_all.deb ...
Unpacking emboss-data (6.6.0+dfsg-12) ...
Selecting previously unselected package emboss.
Preparing to unpack .../065-emboss_6.6.0+dfsg-12_armhf.deb ...
Unpacking emboss (6.6.0+dfsg-12) ...
Selecting previously unselected package fasttree.
Preparing to unpack .../066-fasttree_2.1.11-2_armhf.deb ...
Unpacking fasttree (2.1.11-2) ...
Selecting previously unselected package fonts-lmodern.
Preparing to unpack .../067-fonts-lmodern_2.005-1_all.deb ...
Unpacking fonts-lmodern (2.005-1) ...
Selecting previously unselected package fonts-lyx.
Preparing to unpack .../068-fonts-lyx_2.3.6.1-1_all.deb ...
Unpacking fonts-lyx (2.3.6.1-1) ...
Selecting previously unselected package libgs-common.
Preparing to unpack .../069-libgs-common_10.0.0~dfsg-9_all.deb ...
Unpacking libgs-common (10.0.0~dfsg-9) ...
Selecting previously unselected package libgs10-common.
Preparing to unpack .../070-libgs10-common_10.0.0~dfsg-9_all.deb ...
Unpacking libgs10-common (10.0.0~dfsg-9) ...
Selecting previously unselected package libavahi-common-data:armhf.
Preparing to unpack .../071-libavahi-common-data_0.8-6+b1_armhf.deb ...
Unpacking libavahi-common-data:armhf (0.8-6+b1) ...
Selecting previously unselected package libavahi-common3:armhf.
Preparing to unpack .../072-libavahi-common3_0.8-6+b1_armhf.deb ...
Unpacking libavahi-common3:armhf (0.8-6+b1) ...
Selecting previously unselected package libdbus-1-3:armhf.
Preparing to unpack .../073-libdbus-1-3_1.14.4-1_armhf.deb ...
Unpacking libdbus-1-3:armhf (1.14.4-1) ...
Selecting previously unselected package libavahi-client3:armhf.
Preparing to unpack .../074-libavahi-client3_0.8-6+b1_armhf.deb ...
Unpacking libavahi-client3:armhf (0.8-6+b1) ...
Selecting previously unselected package libcups2:armhf.
Preparing to unpack .../075-libcups2_2.4.2-1+b1_armhf.deb ...
Unpacking libcups2:armhf (2.4.2-1+b1) ...
Selecting previously unselected package libidn12:armhf.
Preparing to unpack .../076-libidn12_1.41-1_armhf.deb ...
Unpacking libidn12:armhf (1.41-1) ...
Selecting previously unselected package libijs-0.35:armhf.
Preparing to unpack .../077-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 .../078-libjbig2dec0_0.19-3+b2_armhf.deb ...
Unpacking libjbig2dec0:armhf (0.19-3+b2) ...
Selecting previously unselected package libpaper1:armhf.
Preparing to unpack .../079-libpaper1_1.1.28_armhf.deb ...
Unpacking libpaper1:armhf (1.1.28) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../080-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 .../081-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 .../082-libxt6_1%3a1.2.1-1_armhf.deb ...
Unpacking libxt6:armhf (1:1.2.1-1) ...
Selecting previously unselected package libgs10:armhf.
Preparing to unpack .../083-libgs10_10.0.0~dfsg-9_armhf.deb ...
Unpacking libgs10:armhf (10.0.0~dfsg-9) ...
Selecting previously unselected package ghostscript.
Preparing to unpack .../084-ghostscript_10.0.0~dfsg-9_armhf.deb ...
Unpacking ghostscript (10.0.0~dfsg-9) ...
Selecting previously unselected package libnetpbm11:armhf.
Preparing to unpack .../085-libnetpbm11_2%3a10.97.00-2_armhf.deb ...
Unpacking libnetpbm11:armhf (2:10.97.00-2) ...
Selecting previously unselected package netpbm.
Preparing to unpack .../086-netpbm_2%3a10.97.00-2_armhf.deb ...
Unpacking netpbm (2:10.97.00-2) ...
Selecting previously unselected package tex-common.
Preparing to unpack .../087-tex-common_6.18_all.deb ...
Unpacking tex-common (6.18) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../088-libpaper-utils_1.1.28_armhf.deb ...
Unpacking libpaper-utils (1.1.28) ...
Selecting previously unselected package libkpathsea6:armhf.
Preparing to unpack .../089-libkpathsea6_2022.20220321.62855-5_armhf.deb ...
Unpacking libkpathsea6:armhf (2022.20220321.62855-5) ...
Selecting previously unselected package libptexenc1:armhf.
Preparing to unpack .../090-libptexenc1_2022.20220321.62855-5_armhf.deb ...
Unpacking libptexenc1:armhf (2022.20220321.62855-5) ...
Selecting previously unselected package libsynctex2:armhf.
Preparing to unpack .../091-libsynctex2_2022.20220321.62855-5_armhf.deb ...
Unpacking libsynctex2:armhf (2022.20220321.62855-5) ...
Selecting previously unselected package libtexlua53-5:armhf.
Preparing to unpack .../092-libtexlua53-5_2022.20220321.62855-5_armhf.deb ...
Unpacking libtexlua53-5:armhf (2022.20220321.62855-5) ...
Selecting previously unselected package libtexluajit2:armhf.
Preparing to unpack .../093-libtexluajit2_2022.20220321.62855-5_armhf.deb ...
Unpacking libtexluajit2:armhf (2022.20220321.62855-5) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../094-t1utils_1.41-4_armhf.deb ...
Unpacking t1utils (1.41-4) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../095-libpixman-1-0_0.42.2-1_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.42.2-1) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../096-libxcb-render0_1.15-1_armhf.deb ...
Unpacking libxcb-render0:armhf (1.15-1) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../097-libxcb-shm0_1.15-1_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.15-1) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../098-libcairo2_1.16.0-7_armhf.deb ...
Unpacking libcairo2:armhf (1.16.0-7) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../099-libgraphite2-3_1.3.14-1_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.14-1) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../100-libharfbuzz0b_5.2.0-2+b1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (5.2.0-2+b1) ...
Selecting previously unselected package libteckit0:armhf.
Preparing to unpack .../101-libteckit0_2.5.11+ds1-1_armhf.deb ...
Unpacking libteckit0:armhf (2.5.11+ds1-1) ...
Selecting previously unselected package libxmu6:armhf.
Preparing to unpack .../102-libxmu6_2%3a1.1.3-3_armhf.deb ...
Unpacking libxmu6:armhf (2:1.1.3-3) ...
Selecting previously unselected package libxaw7:armhf.
Preparing to unpack .../103-libxaw7_2%3a1.0.14-1_armhf.deb ...
Unpacking libxaw7:armhf (2:1.0.14-1) ...
Selecting previously unselected package libxi6:armhf.
Preparing to unpack .../104-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 .../105-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 .../106-texlive-binaries_2022.20220321.62855-5_armhf.deb ...
Unpacking texlive-binaries (2022.20220321.62855-5) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../107-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 .../108-texlive-base_2022.20221123-1_all.deb ...
Unpacking texlive-base (2022.20221123-1) ...
Selecting previously unselected package hicolor-icon-theme.
Preparing to unpack .../109-hicolor-icon-theme_0.17-2_all.deb ...
Unpacking hicolor-icon-theme (0.17-2) ...
Selecting previously unselected package imagemagick-6.q16.
Preparing to unpack .../110-imagemagick-6.q16_8%3a6.9.11.60+dfsg-1.3+b4_armhf.deb ...
Unpacking imagemagick-6.q16 (8:6.9.11.60+dfsg-1.3+b4) ...
Selecting previously unselected package imagemagick.
Preparing to unpack .../111-imagemagick_8%3a6.9.11.60+dfsg-1.3+b4_armhf.deb ...
Unpacking imagemagick (8:6.9.11.60+dfsg-1.3+b4) ...
Selecting previously unselected package hevea.
Preparing to unpack .../112-hevea_2.36-1+b3_armhf.deb ...
Unpacking hevea (2.36-1+b3) ...
Selecting previously unselected package libapache-pom-java.
Preparing to unpack .../113-libapache-pom-java_25-2_all.deb ...
Unpacking libapache-pom-java (25-2) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../114-libblas3_3.10.1-2_armhf.deb ...
Unpacking libblas3:armhf (3.10.1-2) ...
Selecting previously unselected package libcommons-parent-java.
Preparing to unpack .../115-libcommons-parent-java_43-1_all.deb ...
Unpacking libcommons-parent-java (43-1) ...
Selecting previously unselected package libcommons-logging-java.
Preparing to unpack .../116-libcommons-logging-java_1.2-3_all.deb ...
Unpacking libcommons-logging-java (1.2-3) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../117-libnghttp2-14_1.51.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.51.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../118-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 .../119-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 .../120-libssh2-1_1.10.0-3+b1_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-3+b1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../121-libcurl3-gnutls_7.86.0-2_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.86.0-2) ...
Selecting previously unselected package libexpat1-dev:armhf.
Preparing to unpack .../122-libexpat1-dev_2.5.0-1_armhf.deb ...
Unpacking libexpat1-dev:armhf (2.5.0-1) ...
Selecting previously unselected package libfontbox-java.
Preparing to unpack .../123-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 .../124-libfribidi0_1.0.8-2.1_armhf.deb ...
Unpacking libfribidi0:armhf (1.0.8-2.1) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../125-libgfortran5_12.2.0-10+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (12.2.0-10+rpi1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../126-libhtscodecs2_1.3.0-4_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.3.0-4) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../127-libhts3_1.16+ds-3_armhf.deb ...
Unpacking libhts3:armhf (1.16+ds-3) ...
Selecting previously unselected package libimagequant0:armhf.
Preparing to unpack .../128-libimagequant0_2.17.0-1_armhf.deb ...
Unpacking libimagequant0:armhf (2.17.0-1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../129-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../130-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../131-libjs-underscore_1.13.4~dfsg+~1.11.4-2_all.deb ...
Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-2) ...
Selecting previously unselected package libjs-sphinxdoc.
Preparing to unpack .../132-libjs-sphinxdoc_5.3.0-2_all.deb ...
Unpacking libjs-sphinxdoc (5.3.0-2) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../133-liblapack3_3.10.1-2_armhf.deb ...
Unpacking liblapack3:armhf (3.10.1-2) ...
Selecting previously unselected package liblbfgsb0:armhf.
Preparing to unpack .../134-liblbfgsb0_3.0+dfsg.3-11_armhf.deb ...
Unpacking liblbfgsb0:armhf (3.0+dfsg.3-11) ...
Selecting previously unselected package liblmdb0:armhf.
Preparing to unpack .../135-liblmdb0_0.9.24-1_armhf.deb ...
Unpacking liblmdb0:armhf (0.9.24-1) ...
Selecting previously unselected package libmbedcrypto7:armhf.
Preparing to unpack .../136-libmbedcrypto7_2.28.1-1_armhf.deb ...
Unpacking libmbedcrypto7:armhf (2.28.1-1) ...
Selecting previously unselected package libmbedx509-1:armhf.
Preparing to unpack .../137-libmbedx509-1_2.28.1-1_armhf.deb ...
Unpacking libmbedx509-1:armhf (2.28.1-1) ...
Selecting previously unselected package libmbedtls14:armhf.
Preparing to unpack .../138-libmbedtls14_2.28.1-1_armhf.deb ...
Unpacking libmbedtls14:armhf (2.28.1-1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../139-libncurses6_6.3+20220423-2_armhf.deb ...
Unpacking libncurses6:armhf (6.3+20220423-2) ...
Selecting previously unselected package libpdfbox-java.
Preparing to unpack .../140-libpdfbox-java_1%3a1.8.16-2_all.deb ...
Unpacking libpdfbox-java (1:1.8.16-2) ...
Selecting previously unselected package libpython3.10:armhf.
Preparing to unpack .../141-libpython3.10_3.10.9-1_armhf.deb ...
Unpacking libpython3.10:armhf (3.10.9-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../142-zlib1g-dev_1%3a1.2.13.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-1) ...
Selecting previously unselected package libpython3.10-dev:armhf.
Preparing to unpack .../143-libpython3.10-dev_3.10.9-1_armhf.deb ...
Unpacking libpython3.10-dev:armhf (3.10.9-1) ...
Selecting previously unselected package libpython3-dev:armhf.
Preparing to unpack .../144-libpython3-dev_3.10.6-3_armhf.deb ...
Unpacking libpython3-dev:armhf (3.10.6-3) ...
Selecting previously unselected package libpython3.11-stdlib:armhf.
Preparing to unpack .../145-libpython3.11-stdlib_3.11.1-1_armhf.deb ...
Unpacking libpython3.11-stdlib:armhf (3.11.1-1) ...
Selecting previously unselected package libpython3.11:armhf.
Preparing to unpack .../146-libpython3.11_3.11.1-1_armhf.deb ...
Unpacking libpython3.11:armhf (3.11.1-1) ...
Selecting previously unselected package libpython3.11-dev:armhf.
Preparing to unpack .../147-libpython3.11-dev_3.11.1-1_armhf.deb ...
Unpacking libpython3.11-dev:armhf (3.11.1-1) ...
Selecting previously unselected package libpython3-all-dev:armhf.
Preparing to unpack .../148-libpython3-all-dev_3.10.6-3_armhf.deb ...
Unpacking libpython3-all-dev:armhf (3.10.6-3) ...
Selecting previously unselected package libqhull-r8.0:armhf.
Preparing to unpack .../149-libqhull-r8.0_2020.2-5_armhf.deb ...
Unpacking libqhull-r8.0:armhf (2020.2-5) ...
Selecting previously unselected package libraqm0:armhf.
Preparing to unpack .../150-libraqm0_0.7.0-4_armhf.deb ...
Unpacking libraqm0:armhf (0.7.0-4) ...
Selecting previously unselected package libxslt1.1:armhf.
Preparing to unpack .../151-libxslt1.1_1.1.35-1_armhf.deb ...
Unpacking libxslt1.1:armhf (1.1.35-1) ...
Selecting previously unselected package mafft.
Preparing to unpack .../152-mafft_7.505-1_armhf.deb ...
Unpacking mafft (7.505-1) ...
Selecting previously unselected package ncbi-data.
Preparing to unpack .../153-ncbi-data_6.1.20170106+dfsg1-10_all.deb ...
Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
Selecting previously unselected package ncbi-blast+.
Preparing to unpack .../154-ncbi-blast+_2.12.0+ds-3+b2_armhf.deb ...
Unpacking ncbi-blast+ (2.12.0+ds-3+b2) ...
Selecting previously unselected package phylip.
Preparing to unpack .../155-phylip_1%3a3.697+dfsg-2_armhf.deb ...
Unpacking phylip (1:3.697+dfsg-2) ...
Selecting previously unselected package prank.
Preparing to unpack .../156-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 .../157-preview-latex-style_12.2-1_all.deb ...
Unpacking preview-latex-style (12.2-1) ...
Selecting previously unselected package probcons.
Preparing to unpack .../158-probcons_1.12-14_armhf.deb ...
Unpacking probcons (1.12-14) ...
Selecting previously unselected package python-matplotlib-data.
Preparing to unpack .../159-python-matplotlib-data_3.5.2-4_all.deb ...
Unpacking python-matplotlib-data (3.5.2-4) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../160-python3.11_3.11.1-1_armhf.deb ...
Unpacking python3.11 (3.11.1-1) ...
Selecting previously unselected package python3-all.
Preparing to unpack .../161-python3-all_3.10.6-3_armhf.deb ...
Unpacking python3-all (3.10.6-3) ...
Selecting previously unselected package python3.10-dev.
Preparing to unpack .../162-python3.10-dev_3.10.9-1_armhf.deb ...
Unpacking python3.10-dev (3.10.9-1) ...
Selecting previously unselected package python3-dev.
Preparing to unpack .../163-python3-dev_3.10.6-3_armhf.deb ...
Unpacking python3-dev (3.10.6-3) ...
Selecting previously unselected package python3.11-dev.
Preparing to unpack .../164-python3.11-dev_3.11.1-1_armhf.deb ...
Unpacking python3.11-dev (3.11.1-1) ...
Selecting previously unselected package python3-all-dev.
Preparing to unpack .../165-python3-all-dev_3.10.6-3_armhf.deb ...
Unpacking python3-all-dev (3.10.6-3) ...
Selecting previously unselected package python3-appdirs.
Preparing to unpack .../166-python3-appdirs_1.4.4-3_all.deb ...
Unpacking python3-appdirs (1.4.4-3) ...
Selecting previously unselected package python3-attr.
Preparing to unpack .../167-python3-attr_22.2.0-1_all.deb ...
Unpacking python3-attr (22.2.0-1) ...
Selecting previously unselected package python3-brotli.
Preparing to unpack .../168-python3-brotli_1.0.9-2+b2_armhf.deb ...
Unpacking python3-brotli (1.0.9-2+b2) ...
Selecting previously unselected package python3-cycler.
Preparing to unpack .../169-python3-cycler_0.11.0-1_all.deb ...
Unpacking python3-cycler (0.11.0-1) ...
Selecting previously unselected package python3-six.
Preparing to unpack .../170-python3-six_1.16.0-4_all.deb ...
Unpacking python3-six (1.16.0-4) ...
Selecting previously unselected package python3-dateutil.
Preparing to unpack .../171-python3-dateutil_2.8.2-1_all.deb ...
Unpacking python3-dateutil (2.8.2-1) ...
Selecting previously unselected package python3-decorator.
Preparing to unpack .../172-python3-decorator_5.1.1-3_all.deb ...
Unpacking python3-decorator (5.1.1-3) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../173-python3-pkg-resources_65.5.0-1_all.deb ...
Unpacking python3-pkg-resources (65.5.0-1) ...
Selecting previously unselected package python3-numpy.
Preparing to unpack .../174-python3-numpy_1%3a1.23.5-2+b1_armhf.deb ...
Unpacking python3-numpy (1:1.23.5-2+b1) ...
Selecting previously unselected package python3-scipy.
Preparing to unpack .../175-python3-scipy_1.8.1-14+rpi1_armhf.deb ...
Unpacking python3-scipy (1.8.1-14+rpi1) ...
Selecting previously unselected package python3-ufolib2.
Preparing to unpack .../176-python3-ufolib2_0.13.1+dfsg1-1_all.deb ...
Unpacking python3-ufolib2 (0.13.1+dfsg1-1) ...
Selecting previously unselected package python3-mpmath.
Preparing to unpack .../177-python3-mpmath_1.2.1-2_all.deb ...
Unpacking python3-mpmath (1.2.1-2) ...
Selecting previously unselected package python3-sympy.
Preparing to unpack .../178-python3-sympy_1.11.1-1_all.deb ...
Unpacking python3-sympy (1.11.1-1) ...
Selecting previously unselected package python3-tz.
Preparing to unpack .../179-python3-tz_2022.6-1_all.deb ...
Unpacking python3-tz (2022.6-1) ...
Selecting previously unselected package python3-fs.
Preparing to unpack .../180-python3-fs_2.4.16-2_all.deb ...
Unpacking python3-fs (2.4.16-2) ...
Selecting previously unselected package python3-lxml:armhf.
Preparing to unpack .../181-python3-lxml_4.9.1-1_armhf.deb ...
Unpacking python3-lxml:armhf (4.9.1-1) ...
Selecting previously unselected package python3-lz4.
Preparing to unpack .../182-python3-lz4_4.0.2+dfsg-1_armhf.deb ...
Unpacking python3-lz4 (4.0.2+dfsg-1) ...
Selecting previously unselected package python3-unicodedata2.
Preparing to unpack .../183-python3-unicodedata2_14.0.0+ds2-1_armhf.deb ...
Unpacking python3-unicodedata2 (14.0.0+ds2-1) ...
Selecting previously unselected package unicode-data.
Preparing to unpack .../184-unicode-data_15.0.0-1_all.deb ...
Unpacking unicode-data (15.0.0-1) ...
Selecting previously unselected package python3-fonttools.
Preparing to unpack .../185-python3-fonttools_4.37.4-1_armhf.deb ...
Unpacking python3-fonttools (4.37.4-1) ...
Selecting previously unselected package python3-isodate.
Preparing to unpack .../186-python3-isodate_0.6.1-1_all.deb ...
Unpacking python3-isodate (0.6.1-1) ...
Selecting previously unselected package python3-kiwisolver.
Preparing to unpack .../187-python3-kiwisolver_1.3.2-1+b1_armhf.deb ...
Unpacking python3-kiwisolver (1.3.2-1+b1) ...
Selecting previously unselected package python3-pil:armhf.
Preparing to unpack .../188-python3-pil_9.2.0-1.1_armhf.deb ...
Unpacking python3-pil:armhf (9.2.0-1.1) ...
Selecting previously unselected package python3-tk:armhf.
Preparing to unpack .../189-python3-tk_3.10.8-1_armhf.deb ...
Unpacking python3-tk:armhf (3.10.8-1) ...
Selecting previously unselected package python3-pil.imagetk:armhf.
Preparing to unpack .../190-python3-pil.imagetk_9.2.0-1.1_armhf.deb ...
Unpacking python3-pil.imagetk:armhf (9.2.0-1.1) ...
Selecting previously unselected package python3-pyparsing.
Preparing to unpack .../191-python3-pyparsing_3.0.9-1_all.deb ...
Unpacking python3-pyparsing (3.0.9-1) ...
Selecting previously unselected package python3-packaging.
Preparing to unpack .../192-python3-packaging_21.3-1.1_all.deb ...
Unpacking python3-packaging (21.3-1.1) ...
Selecting previously unselected package python3-matplotlib.
Preparing to unpack .../193-python3-matplotlib_3.5.2-4_armhf.deb ...
Unpacking python3-matplotlib (3.5.2-4) ...
Selecting previously unselected package python3-msgpack.
Preparing to unpack .../194-python3-msgpack_1.0.3-2_armhf.deb ...
Unpacking python3-msgpack (1.0.3-2) ...
Selecting previously unselected package python3-mmtf.
Preparing to unpack .../195-python3-mmtf_1.1.3-1_all.deb ...
Unpacking python3-mmtf (1.1.3-1) ...
Selecting previously unselected package python3-mysqldb.
Preparing to unpack .../196-python3-mysqldb_1.4.6-2_armhf.deb ...
Unpacking python3-mysqldb (1.4.6-2) ...
Selecting previously unselected package python3-networkx.
Preparing to unpack .../197-python3-networkx_2.6.3-1_all.deb ...
Unpacking python3-networkx (2.6.3-1) ...
Selecting previously unselected package python3-psycopg2.
Preparing to unpack .../198-python3-psycopg2_2.9.4-2_armhf.deb ...
Unpacking python3-psycopg2 (2.9.4-2) ...
Selecting previously unselected package python3-pygments.
Preparing to unpack .../199-python3-pygments_2.13.0+dfsg-1_all.deb ...
Unpacking python3-pygments (2.13.0+dfsg-1) ...
Selecting previously unselected package python3-rdflib.
Preparing to unpack .../200-python3-rdflib_6.1.1-1_all.deb ...
Unpacking python3-rdflib (6.1.1-1) ...
Selecting previously unselected package python3-renderpm:armhf.
Preparing to unpack .../201-python3-renderpm_3.6.11-1_armhf.deb ...
Unpacking python3-renderpm:armhf (3.6.11-1) ...
Selecting previously unselected package python3-reportlab-accel:armhf.
Preparing to unpack .../202-python3-reportlab-accel_3.6.11-1_armhf.deb ...
Unpacking python3-reportlab-accel:armhf (3.6.11-1) ...
Selecting previously unselected package python3-reportlab.
Preparing to unpack .../203-python3-reportlab_3.6.11-1_all.deb ...
Unpacking python3-reportlab (3.6.11-1) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../204-python3-setuptools_65.5.0-1_all.deb ...
Unpacking python3-setuptools (65.5.0-1) ...
Selecting previously unselected package python3-unittest2.
Preparing to unpack .../205-python3-unittest2_1.1.0-9_all.deb ...
Unpacking python3-unittest2 (1.1.0-9) ...
Selecting previously unselected package samtools.
Preparing to unpack .../206-samtools_1.16.1-1_armhf.deb ...
Unpacking samtools (1.16.1-1) ...
Selecting previously unselected package t-coffee.
Preparing to unpack .../207-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.deb ...
Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ...
Selecting previously unselected package texlive-fonts-recommended.
Preparing to unpack .../208-texlive-fonts-recommended_2022.20221123-1_all.deb ...
Unpacking texlive-fonts-recommended (2022.20221123-1) ...
Selecting previously unselected package texlive-latex-base.
Preparing to unpack .../209-texlive-latex-base_2022.20221123-1_all.deb ...
Unpacking texlive-latex-base (2022.20221123-1) ...
Selecting previously unselected package texlive-latex-recommended.
Preparing to unpack .../210-texlive-latex-recommended_2022.20221123-1_all.deb ...
Unpacking texlive-latex-recommended (2022.20221123-1) ...
Selecting previously unselected package texlive-pictures.
Preparing to unpack .../211-texlive-pictures_2022.20221123-1_all.deb ...
Unpacking texlive-pictures (2022.20221123-1) ...
Selecting previously unselected package texlive-latex-extra.
Preparing to unpack .../212-texlive-latex-extra_2022.20221123-2_all.deb ...
Unpacking texlive-latex-extra (2022.20221123-2) ...
Selecting previously unselected package wise-data.
Preparing to unpack .../213-wise-data_2.4.1-23_all.deb ...
Unpacking wise-data (2.4.1-23) ...
Selecting previously unselected package wise.
Preparing to unpack .../214-wise_2.4.1-23_armhf.deb ...
Unpacking wise (2.4.1-23) ...
Selecting previously unselected package sbuild-build-depends-python-biopython-dummy.
Preparing to unpack .../215-sbuild-build-depends-python-biopython-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-python-biopython-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.3.0-4) ...
Setting up media-types (8.0.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up liblmdb0:armhf (0.9.24-1) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up liblcms2-2:armhf (2.13.1-1) ...
Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
Setting up libpixman-1-0:armhf (0.42.2-1) ...
Setting up libaom3:armhf (3.5.0-1) ...
Setting up mysql-common (5.8+1.0.8) ...
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 imagemagick-6-common (8:6.9.11.60+dfsg-1.3) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up libicu72:armhf (72.1-3) ...
Setting up liblerc4:armhf (4.0.0+ds-2) ...
Setting up bsdextrautils (2.38.1-4) ...
Setting up hicolor-icon-theme (0.17-2) ...
Setting up probcons (1.12-14) ...
Setting up libmagic-mgc (1:5.41-4) ...
Setting up mafft (7.505-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.74.1-2) ...
No schema files found: doing nothing.
Setting up bwa (0.7.17-7) ...
Setting up libboost-iostreams1.74.0:armhf (1.74.0-18) ...
Setting up libboost-program-options1.74.0:armhf (1.74.0-18) ...
Setting up fonts-lyx (2.3.6.1-1) ...
Setting up libijs-0.35:armhf (0.35-15) ...
Setting up libtexluajit2:armhf (2022.20220321.62855-5) ...
Setting up libdebhelper-perl (13.11.3) ...
Setting up libgs-common (10.0.0~dfsg-9) ...
Setting up libbrotli1:armhf (1.0.9-2+b2) ...
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
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up libnghttp2-14:armhf (1.51.0-1) ...
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up libpq5:armhf (15.1-1) ...
Setting up libnetpbm11:armhf (2:10.97.00-2) ...
Setting up libdeflate0:armhf (1.14-1) ...
Setting up gettext-base (0.21-10) ...
Setting up m4 (1.4.19-1) ...
Setting up libqhull-r8.0:armhf (2020.2-5) ...
Setting up libzzip-0-13:armhf (0.13.72+dfsg.1-1.1) ...
Setting up file (1:5.41-4) ...
Setting up libsvtav1enc1:armhf (1.4.1+dfsg-1) ...
Setting up emboss-data (6.6.0+dfsg-12) ...
Setting up libjbig0:armhf (2.1-6.1) ...
Setting up librav1e0:armhf (0.5.1-5) ...
Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ...
Setting up poppler-data (0.4.11-1) ...
Setting up unicode-data (15.0.0-1) ...
Setting up mariadb-common (1:10.6.11-1) ...
update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Setting up libfontenc1:armhf (1:1.1.4-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libexpat1-dev:armhf (2.5.0-1) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up libmbedcrypto7:armhf (2.28.1-1) ...
Setting up libx11-data (2:1.8.1-2) ...
Setting up libjbig2dec0:armhf (0.19-3+b2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libteckit0:armhf (2.5.11+ds1-1) ...
Setting up libapache-pom-java (25-2) ...
Setting up libavahi-common-data:armhf (0.8-6+b1) ...
Setting up libncurses6:armhf (6.3+20220423-2) ...
Setting up libdbus-1-3:armhf (1.14.4-1) ...
Setting up xfonts-encodings (1:1.0.4-2.1) ...
Setting up libfribidi0:armhf (1.0.8-2.1) ...
Setting up libboost-regex1.74.0:armhf (1.74.0-18) ...
Setting up t1utils (1.41-4) ...
Setting up libtexlua53-5:armhf (2022.20220321.62855-5) ...
Setting up libimagequant0:armhf (2.17.0-1) ...
Setting up libpng16-16:armhf (1.6.39-2) ...
Setting up libidn12:armhf (1.41-1) ...
Setting up libtcl8.6:armhf (8.6.13+dfsg-1) ...
Setting up autopoint (0.21-10) ...
Setting up libmariadb3:armhf (1:10.6.11-1) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up libabsl20210324:armhf (0~20210324.2-4+rpi1) ...
Setting up ucf (3.0043) ...
Setting up wise-data (2.4.1-23) ...
Setting up libdav1d6:armhf (1.0.0-2+rpi1) ...
Setting up libltdl7:armhf (2.4.7-5) ...
Setting up libfftw3-double3:armhf (3.3.10-1) ...
Setting up libcifpp-data (2.0.5-4) ...
Setting up libkpathsea6:armhf (2022.20220321.62855-5) ...
Setting up libgfortran5:armhf (12.2.0-10+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up libx265-199:armhf (3.5-2) ...
Setting up libwebp7:armhf (1.2.2-2+b1) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ...
Setting up libmd0:armhf (1.0.4-2) ...
Setting up liblqr-1-0:armhf (0.4.2-2.1) ...
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 (2.005-1) ...
Setting up libopenjp2-7:armhf (2.5.0-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up fasttree (2.1.11-2) ...
Setting up libtiff5:armhf (4.4.0-6) ...
Setting up libpython3.11-minimal:armhf (3.11.1-1) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libde265-0:armhf (1.0.9-1+rpi1) ...
Setting up python-matplotlib-data (3.5.2-4) ...
Setting up libwebpmux3:armhf (1.2.2-2+b1) ...
Setting up libbsd0:armhf (0.11.7-1) ...
Setting up libyuv0:armhf (0.0~git20221118.ea26d7a-2) ...
Setting up mailcap (3.70+nmu1) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up dialign (2.2.1-11) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.1) ...
Setting up xdg-utils (1.1.3-4.1) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libsynctex2:armhf (2022.20220321.62855-5) ...
Setting up prank (0.0.170427+dfsg-3) ...
Setting up libargtable2-0 (13-1.1) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-2) ...
Setting up python3.11-minimal (3.11.1-1) ...
Setting up libpaper1:armhf (1.1.28) ...

Creating config file /etc/papersize with new version
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 flex (2.6.4-8.1) ...
Setting up liblapack3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-10) ...
Setting up libpdfbox-java (1:1.8.16-2) ...
Setting up mime-support (3.66) ...
Setting up libmbedx509-1:armhf (2.28.1-1) ...
Setting up libmbedtls14:armhf (2.28.1-1) ...
Setting up libtool (2.4.7-5) ...
Setting up libxcb-render0:armhf (1.15-1) ...
Setting up fontconfig-config (2.13.1-4.5) ...
Setting up wise (2.4.1-23) ...
Setting up libwebpdemux2:armhf (1.2.2-2+b1) ...
Setting up libpython3.11-stdlib:armhf (3.11.1-1) ...
Setting up libheif1:armhf (1.13.0-1) ...
Setting up libcommons-parent-java (43-1) ...
Setting up libavahi-common3:armhf (0.8-6+b1) ...
Setting up libcommons-logging-java (1.2-3) ...
Setting up libcurl3-gnutls:armhf (7.86.0-2) ...
Setting up libxcb-shm0:armhf (1.15-1) ...
Setting up libpaper-utils (1.1.28) ...
Setting up clustalo (1.2.4-7) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libpython3.10-stdlib:armhf (3.10.9-1) ...
Setting up dh-autoreconf (20) ...
Setting up tex-common (6.18) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libptexenc1:armhf (2022.20220321.62855-5) ...
Setting up libcifpp2:armhf (2.0.5-4+b1) ...
Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up libgav1-1:armhf (0.18.0-1+rpi1) ...
Setting up libjs-sphinxdoc (5.3.0-2) ...
Setting up dh-strip-nondeterminism (1.13.0-2) ...
Setting up dwz (0.14+20220924-2) ...
Setting up groff-base (1.22.4-9) ...
Setting up libxslt1.1:armhf (1.1.35-1) ...
Setting up libx11-6:armhf (2:1.8.1-2) ...
Setting up libharfbuzz0b:armhf (5.2.0-2+b1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libavahi-client3:armhf (0.8-6+b1) ...
Setting up libpython3-stdlib:armhf (3.10.6-3) ...
Setting up liblbfgsb0:armhf (3.0+dfsg.3-11) ...
Setting up python3.11 (3.11.1-1) ...
Setting up libpython3.10:armhf (3.10.9-1) ...
Setting up libhts3:armhf (1.16+ds-3) ...
Setting up python3.10 (3.10.9-1) ...
Setting up libpython3.11:armhf (3.11.1-1) ...
Setting up libxpm4:armhf (1:3.5.12-1) ...
Setting up libavif15:armhf (0.11.1-1) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up preview-latex-style (12.2-1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up python3 (3.10.6-3) ...
Setting up dssp (4.0.4-1) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up man-db (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python3-tz (2022.6-1) ...
Setting up samtools (1.16.1-1) ...
Setting up ncbi-blast+ (2.12.0+ds-3+b2) ...
Setting up python3-mysqldb (1.4.6-2) ...
Setting up python3-six (1.16.0-4) ...
Setting up python3-isodate (0.6.1-1) ...
Setting up python3-decorator (5.1.1-3) ...
Setting up python3-pyparsing (3.0.9-1) ...
Setting up libpython3.11-dev:armhf (3.11.1-1) ...
Setting up python3-brotli (1.0.9-2+b2) ...
Setting up libraqm0:armhf (0.7.0-4) ...
Setting up python3-cycler (0.11.0-1) ...
Setting up python3-reportlab-accel:armhf (3.6.11-1) ...
Setting up python3-kiwisolver (1.3.2-1+b1) ...
Setting up python3-psycopg2 (2.9.4-2) ...
Setting up libpython3.10-dev:armhf (3.10.9-1) ...
Setting up netpbm (2:10.97.00-2) ...
Setting up libxt6:armhf (1:1.2.1-1) ...
Setting up libcups2:armhf (2.4.2-1+b1) ...
Setting up python3.10-dev (3.10.9-1) ...
Setting up python3-lxml:armhf (4.9.1-1) ...
Setting up python3-dateutil (2.8.2-1) ...
Setting up python3-msgpack (1.0.3-2) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up python3-mpmath (1.2.1-2) ...
Setting up python3-lib2to3 (3.10.8-1) ...
Setting up python3-appdirs (1.4.4-3) ...
Setting up python3-pkg-resources (65.5.0-1) ...
Setting up python3-distutils (3.10.8-1) ...
Setting up dh-python (5.20220819+rpi1) ...
Setting up python3-sympy (1.11.1-1) ...
Setting up python3-attr (22.2.0-1) ...
Setting up libxmu6:armhf (2:1.1.3-3) ...
Setting up libpython3-dev:armhf (3.10.6-3) ...
Setting up python3-setuptools (65.5.0-1) ...
Setting up libxi6:armhf (2:1.8-1) ...
Setting up python3-lz4 (4.0.2+dfsg-1) ...
Setting up python3.11-dev (3.11.1-1) ...
Setting up python3-unicodedata2 (14.0.0+ds2-1) ...
Setting up python3-all (3.10.6-3) ...
Setting up debhelper (13.11.3) ...
Setting up libxaw7:armhf (2:1.0.14-1) ...
Setting up fonts-urw-base35 (20200910-6) ...
Setting up python3-networkx (2.6.3-1) ...
Setting up python3-fs (2.4.16-2) ...
Setting up python3-pil:armhf (9.2.0-1.1) ...
Setting up python3-pygments (2.13.0+dfsg-1) ...
Setting up python3-packaging (21.3-1.1) ...
Setting up libpython3-all-dev:armhf (3.10.6-3) ...
Setting up python3-dev (3.10.6-3) ...
Setting up python3-unittest2 (1.1.0-9) ...
update-alternatives: using /usr/bin/python3-unit2 to provide /usr/bin/unit2 (unit2) in auto mode
Setting up python3-numpy (1:1.23.5-2+b1) ...
Setting up python3-reportlab (3.6.11-1) ...
Setting up python3-rdflib (6.1.1-1) ...
Setting up python3-all-dev (3.10.6-3) ...
Setting up libgs10-common (10.0.0~dfsg-9) ...
Setting up python3-scipy (1.8.1-14+rpi1) ...
Setting up python3-renderpm:armhf (3.6.11-1) ...
Setting up python3-mmtf (1.1.3-1) ...
Setting up python3-fonttools (4.37.4-1) ...
Setting up python3-ufolib2 (0.13.1+dfsg1-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up libgs10:armhf (10.0.0~dfsg-9) ...
Setting up libxft2:armhf (2.3.6-1) ...
Setting up libtk8.6:armhf (8.6.13-1) ...
Processing triggers for libc-bin (2.36-6+rpi1) ...
Setting up ghostscript (10.0.0~dfsg-9) ...
Setting up libcairo2:armhf (1.16.0-7) ...
Setting up libmagickcore-6.q16-6:armhf (8:6.9.11.60+dfsg-1.3+b4) ...
Setting up libgd3:armhf (2.3.3-7) ...
Setting up texlive-binaries (2022.20220321.62855-5) ...
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 libmagickwand-6.q16-6:armhf (8:6.9.11.60+dfsg-1.3+b4) ...
Setting up emboss-lib (6.6.0+dfsg-12) ...
Setting up texlive-base (2022.20221123-1) ...
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 tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Setting up emboss (6.6.0+dfsg-12) ...
Setting up blt (2.5.3+dfsg-4.1) ...
Setting up python3-tk:armhf (3.10.8-1) ...
Setting up texlive-latex-base (2022.20221123-1) ...
Setting up python3-pil.imagetk:armhf (9.2.0-1.1) ...
Setting up texlive-latex-recommended (2022.20221123-1) ...
Setting up texlive-pictures (2022.20221123-1) ...
Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.3+b4) ...
update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode
update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode
update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode
update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode
update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode
update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode
update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode
update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode
update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode
update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode
update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode
update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode
update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode
update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode
update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode
update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode
update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode
update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode
update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode
update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode
update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode
update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode
Setting up texlive-fonts-recommended (2022.20221123-1) ...
Setting up python3-matplotlib (3.5.2-4) ...
Setting up texlive-latex-extra (2022.20221123-2) ...
Setting up hevea (2.36-1+b3) ...
Setting up imagemagick (8:6.9.11.60+dfsg-1.3+b4) ...
Setting up sbuild-build-depends-python-biopython-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.36-6+rpi1) ...
Processing triggers for tex-common (6.18) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.39.50.20221208-5+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-10+rpi1 gcc-12_12.2.0-10+rpi1 libc6-dev_2.36-6+rpi1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 linux-libc-dev_6.0.12-1+rpi1
Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2-2 binutils_2.39.50.20221208-5+rpi1 binutils-arm-linux-gnueabihf_2.39.50.20221208-5+rpi1 binutils-common_2.39.50.20221208-5+rpi1 blt_2.5.3+dfsg-4.1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bwa_0.7.17-7 bzip2_1.0.8-5+b2 clustalo_1.2.4-7 clustalw_2.1+lgpl-7 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.3 debianutils_5.7-0.4 dh-autoreconf_20 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-2 dialign_2.2.1-11 diffutils_1:3.8-1 dirmngr_2.2.40-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dssp_4.0.4-1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 emboss_6.6.0+dfsg-12 emboss-data_6.6.0+dfsg-12 emboss-lib_6.6.0+dfsg-12 fakeroot_1.29-1 fasttree_2.1.11-2 file_1:5.41-4 findutils_4.9.0-3 flex_2.6.4-8.1 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 fonts-lmodern_2.005-1 fonts-lyx_2.3.6.1-1 fonts-urw-base35_20200910-6 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-10+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-10+rpi1 gcc-12-base_12.2.0-10+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_0.21-10 gettext-base_0.21-10 ghostscript_10.0.0~dfsg-9 gnupg_2.2.40-1 gnupg-l10n_2.2.40-1 gnupg-utils_2.2.40-1 gpg_2.2.40-1 gpg-agent_2.2.40-1 gpg-wks-client_2.2.40-1 gpg-wks-server_2.2.40-1 gpgconf_2.2.40-1 gpgsm_2.2.40-1 gpgv_2.2.40-1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1 hevea_2.36-1+b3 hicolor-icon-theme_0.17-2 hostname_3.23 imagemagick_8:6.9.11.60+dfsg-1.3+b4 imagemagick-6-common_8:6.9.11.60+dfsg-1.3 imagemagick-6.q16_8:6.9.11.60+dfsg-1.3+b4 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-1 libabsl20210324_0~20210324.2-4+rpi1 libacl1_2.3.1-2 libaom3_3.5.0-1 libapache-pom-java_25-2 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libargtable2-0_13-1.1 libasan8_12.2.0-10+rpi1 libassuan0_2.5.5-5 libatomic1_12.2.0-10+rpi1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libavahi-client3_0.8-6+b1 libavahi-common-data_0.8-6+b1 libavahi-common3_0.8-6+b1 libavif15_0.11.1-1 libbinutils_2.39.50.20221208-5+rpi1 libblas3_3.10.1-2 libblkid1_2.38.1-4 libboost-iostreams1.74.0_1.74.0-18 libboost-program-options1.74.0_1.74.0-18 libboost-regex1.74.0_1.74.0-18 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-6+rpi1 libc-dev-bin_2.36-6+rpi1 libc6_2.36-6+rpi1 libc6-dev_2.36-6+rpi1 libcairo2_1.16.0-7 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-10+rpi1 libcifpp-data_2.0.5-4 libcifpp2_2.0.5-4+b1 libcom-err2_1.46.6~rc1-1 libcommons-logging-java_1.2-3 libcommons-parent-java_43-1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libctf-nobfd0_2.39.50.20221208-5+rpi1 libctf0_2.39.50.20221208-5+rpi1 libcups2_2.4.2-1+b1 libcurl3-gnutls_7.86.0-2 libdav1d6_1.0.0-2+rpi1 libdb5.3_5.3.28+dfsg1-0.10 libdbus-1-3_1.14.4-1 libde265-0_1.0.9-1+rpi1 libdebconfclient0_0.265 libdebhelper-perl_13.11.3 libdeflate0_1.14-1 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libexpat1_2.5.0-1 libexpat1-dev_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.4-1 libfftw3-double3_3.3.10-1 libfile-stripnondeterminism-perl_1.13.0-2 libfontbox-java_1:1.8.16-2 libfontconfig1_2.13.1-4.5 libfontenc1_1:1.1.4-1 libfreetype6_2.12.1+dfsg-3 libfribidi0_1.0.8-2.1 libgav1-1_0.18.0-1+rpi1 libgcc-12-dev_12.2.0-10+rpi1 libgcc-s1_12.2.0-10+rpi1 libgcrypt20_1.10.1-3 libgd3_2.3.3-7 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-10+rpi1 libglib2.0-0_2.74.1-2 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-4 libgomp1_12.2.0-10+rpi1 libgpg-error0_1.46-1 libgraphite2-3_1.3.14-1 libgs-common_10.0.0~dfsg-9 libgs10_10.0.0~dfsg-9 libgs10-common_10.0.0~dfsg-9 libgssapi-krb5-2_1.20.1-1 libharfbuzz0b_5.2.0-2+b1 libheif1_1.13.0-1 libhogweed6_3.8.1-2 libhpdf-2.3.0_2.3.0+dfsg-1 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libice6_2:1.0.10-1 libicu72_72.1-3 libidn12_1.41-1 libidn2-0_2.3.3-1 libijs-0.35_0.35-15 libimagequant0_2.17.0-1 libisl23_0.25-1 libjansson4_2.14-2 libjbig0_2.1-6.1 libjbig2dec0_0.19-3+b2 libjpeg62-turbo_1:2.1.2-1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_5.3.0-2 libjs-underscore_1.13.4~dfsg+~1.11.4-2 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libkpathsea6_2022.20220321.62855-5 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 libksba8_1.6.2-4 liblapack3_3.10.1-2 liblbfgsb0_3.0+dfsg.3-11 liblcms2-2_2.13.1-1 libldap-2.5-0_2.5.13+dfsg-2+rpi1+b1 liblerc4_4.0.0+ds-2 liblmdb0_0.9.24-1 liblqr-1-0_0.4.2-2.1 libltdl7_2.4.7-5 liblz4-1_1.9.4-1+rpi1 liblzma5_5.4.0-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmagickcore-6.q16-6_8:6.9.11.60+dfsg-1.3+b4 libmagickwand-6.q16-6_8:6.9.11.60+dfsg-1.3+b4 libmariadb3_1:10.6.11-1 libmbedcrypto7_2.28.1-1 libmbedtls14_2.28.1-1 libmbedx509-1_2.28.1-1 libmd0_1.0.4-2 libmount1_2.38.1-4 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnetpbm11_2:10.97.00-2 libnettle8_3.8.1-2 libnghttp2-14_1.51.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenjp2-7_2.5.0-1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-8-0_10.40-3 libpcre3_2:8.39-14 libpdfbox-java_1:1.8.16-2 libperl5.36_5.36.0-6 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpng16-16_1.6.39-2 libpq5_15.1-1 libpsl5_0.21.0-1.2 libptexenc1_2022.20220321.62855-5 libpython3-all-dev_3.10.6-3 libpython3-dev_3.10.6-3 libpython3-stdlib_3.10.6-3 libpython3.10_3.10.9-1 libpython3.10-dev_3.10.9-1 libpython3.10-minimal_3.10.9-1 libpython3.10-stdlib_3.10.9-1 libpython3.11_3.11.1-1 libpython3.11-dev_3.11.1-1 libpython3.11-minimal_3.11.1-1 libpython3.11-stdlib_3.11.1-1 libqhull-r8.0_2020.2-5 libraqm0_0.7.0-4 librav1e0_0.5.1-5 libreadline8_8.2-1.2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsm6_2:1.2.3-1 libsmartcols1_2.38.1-4 libsqlite3-0_3.40.0-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 libsub-override-perl_0.09-4 libsvtav1enc1_1.4.1+dfsg-1 libsynctex2_2022.20220321.62855-5 libsystemd0_252.2-1+rpi1 libtasn1-6_4.19.0-2 libtcl8.6_8.6.13+dfsg-1 libteckit0_2.5.11+ds1-1 libtexlua53-5_2022.20220321.62855-5 libtexluajit2_2022.20220321.62855-5 libtiff5_4.4.0-6 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtk8.6_8.6.13-1 libtool_2.4.7-5 libubsan1_12.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_252.2-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-4 libwebp7_1.2.2-2+b1 libwebpdemux2_1.2.2-2+b1 libwebpmux3_1.2.2-2+b1 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libx265-199_3.5-2 libxau6_1:1.0.9-1 libxaw7_2:1.0.14-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxft2_2.3.6-1 libxi6_2:1.8-1 libxml2_2.9.14+dfsg-1.1 libxmu6_2:1.1.3-3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1.1 libxslt1.1_1.1.35-1 libxss1_1:1.2.3-1 libxt6_1:1.2.1-1 libxxhash0_0.8.1-1 libyuv0_0.0~git20221118.ea26d7a-2 libzstd1_1.5.2+dfsg-1 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_6.0.12-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 mafft_7.505-1 mailcap_3.70+nmu1 make_4.3-4.1 man-db_2.11.1-1 mariadb-common_1:10.6.11-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mime-support_3.66 mount_2.38.1-4 mysql-common_5.8+1.0.8 nano_7.1-1 ncbi-blast+_2.12.0+ds-3+b2 ncbi-data_6.1.20170106+dfsg1-10 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.4 netpbm_2:10.97.00-2 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-6 perl-base_5.36.0-6 perl-modules-5.36_5.36.0-6 phylip_1:3.697+dfsg-2 pinentry-curses_1.2.1-1 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_3.5.2-4 python3_3.10.6-3 python3-all_3.10.6-3 python3-all-dev_3.10.6-3 python3-appdirs_1.4.4-3 python3-attr_22.2.0-1 python3-brotli_1.0.9-2+b2 python3-cycler_0.11.0-1 python3-dateutil_2.8.2-1 python3-decorator_5.1.1-3 python3-dev_3.10.6-3 python3-distutils_3.10.8-1 python3-fonttools_4.37.4-1 python3-fs_2.4.16-2 python3-isodate_0.6.1-1 python3-kiwisolver_1.3.2-1+b1 python3-lib2to3_3.10.8-1 python3-lxml_4.9.1-1 python3-lz4_4.0.2+dfsg-1 python3-matplotlib_3.5.2-4 python3-minimal_3.10.6-3 python3-mmtf_1.1.3-1 python3-mpmath_1.2.1-2 python3-msgpack_1.0.3-2 python3-mysqldb_1.4.6-2 python3-networkx_2.6.3-1 python3-numpy_1:1.23.5-2+b1 python3-packaging_21.3-1.1 python3-pil_9.2.0-1.1 python3-pil.imagetk_9.2.0-1.1 python3-pkg-resources_65.5.0-1 python3-psycopg2_2.9.4-2 python3-pygments_2.13.0+dfsg-1 python3-pyparsing_3.0.9-1 python3-rdflib_6.1.1-1 python3-renderpm_3.6.11-1 python3-reportlab_3.6.11-1 python3-reportlab-accel_3.6.11-1 python3-scipy_1.8.1-14+rpi1 python3-setuptools_65.5.0-1 python3-six_1.16.0-4 python3-sympy_1.11.1-1 python3-tk_3.10.8-1 python3-tz_2022.6-1 python3-ufolib2_0.13.1+dfsg1-1 python3-unicodedata2_14.0.0+ds2-1 python3-unittest2_1.1.0-9 python3.10_3.10.9-1 python3.10-dev_3.10.9-1 python3.10-minimal_3.10.9-1 python3.11_3.11.1-1 python3.11-dev_3.11.1-1 python3.11-minimal_3.11.1-1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.2 rpcsvc-proto_1.4.3-1 samtools_1.16.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-biopython-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-7 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 t1utils_1.41-4 tar_1.34+dfsg-1 tex-common_6.18 texlive-base_2022.20221123-1 texlive-binaries_2022.20220321.62855-5 texlive-fonts-recommended_2022.20221123-1 texlive-latex-base_2022.20221123-1 texlive-latex-extra_2022.20221123-2 texlive-latex-recommended_2022.20221123-1 texlive-pictures_2022.20221123-1 tk8.6-blt2.5_2.5.3+dfsg-4.1 tzdata_2022f-1 ucf_3.0043 unicode-data_15.0.0-1 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 wise_2.4.1-23 wise-data_2.4.1-23 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xfonts-encodings_1:1.0.4-2.1 xfonts-utils_1:7.7+6 xz-utils_5.4.0-0.1 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.znFmF4GZ/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 23 20:05:43 2022 UTC
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./python-biopython_1.80+dfsg-3.dsc
dpkg-source: info: extracting python-biopython in /<<BUILDDIR>>/python-biopython-1.80+dfsg
dpkg-source: info: unpacking python-biopython_1.80+dfsg.orig.tar.xz
dpkg-source: info: unpacking python-biopython_1.80+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying remove_mathml-qname.patch
dpkg-source: info: applying privacy_breach.patch
dpkg-source: info: applying privacy_breach_ie9.patch
dpkg-source: info: applying fix-use-of-unversioned-python.patch
dpkg-source: info: applying reproduciblebuild.patch
dpkg-source: info: applying croak-on-muscle5.patch
dpkg-source: info: applying muscle3.patch
dpkg-source: info: applying port_tutorial_to_muscle3.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-ea309678-1a4b-41bc-9694-866c6d3c673f
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

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

dpkg-buildpackage: info: source package python-biopython
dpkg-buildpackage: info: source version 1.80+dfsg-3
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 '/<<BUILDDIR>>/python-biopython-1.80+dfsg'
dh_auto_clean
	pybuild --clean -i python{version} -p "3.11 3.10"
I: pybuild base:240: python3.11 setup.py clean 
running clean
removing '/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
I: pybuild base:240: python3.10 setup.py clean 
running clean
removing '/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.10' does not exist -- can't clean it
	rm -rf .pybuild/
	find . -name \*.pyc -exec rm {} \;
cd Doc && make distclean
make[2]: Entering directory '/<<BUILDDIR>>/python-biopython-1.80+dfsg/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 '/<<BUILDDIR>>/python-biopython-1.80+dfsg/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 '/<<BUILDDIR>>/python-biopython-1.80+dfsg'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/python3-biopython.substvars debian/python-biopython-doc.substvars debian/python3-biopython-sql.substvars debian/files
	rm -fr -- debian/python3-biopython/ debian/tmp/ debian/python-biopython-doc/ debian/python3-biopython-sql/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
 debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
	pybuild --configure -i python{version} -p "3.11 3.10"
I: pybuild base:240: python3.11 setup.py config 
running config
I: pybuild base:240: python3.10 setup.py config 
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/python-biopython-1.80+dfsg'
dh_auto_build
	pybuild --build -i python{version} -p "3.11 3.10"
I: pybuild base:240: /usr/bin/python3.11 setup.py build 
running build
running build_py
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/File.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/LogisticRegression.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/MarkovModel.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/MaxEntropy.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/NaiveBayes.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/Seq.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/SeqFeature.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/SeqRecord.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/_utils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/bgzf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/kNN.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/pairwise2.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Affy
copying Bio/Affy/CelFile.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Affy
copying Bio/Affy/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Affy
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/AlignInfo.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/a2m.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/bed.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/bigbed.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/bigmaf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/bigpsl.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/clustal.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/emboss.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/exonerate.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/fasta.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/hhr.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/interfaces.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/maf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/mauve.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/msf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/nexus.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/phylip.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/psl.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/sam.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/stockholm.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
copying Bio/Align/tabular.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/Applications
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices
copying Bio/Align/substitution_matrices/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/MsfIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/AlignIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Alphabet
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Application
copying Bio/Application/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Application
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/Applications.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/NCBIXML.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/Record.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Blast
copying Bio/Blast/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Blast
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/CAPS
copying Bio/CAPS/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/CAPS
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Cluster
copying Bio/Cluster/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Cluster
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/codonalign
copying Bio/codonalign/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/codonalign
copying Bio/codonalign/codonseq.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/codonalign
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Compass
copying Bio/Compass/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Compass
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/CodonTable.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/IUPACData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/PDBData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/SCOPData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Data
copying Bio/Data/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Data
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Emboss
copying Bio/Emboss/Applications.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Emboss
copying Bio/Emboss/Primer3.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Emboss
copying Bio/Emboss/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Emboss
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez
copying Bio/Entrez/Parser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez
copying Bio/Entrez/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/ExPASy
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/GenBank
copying Bio/GenBank/Record.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/GenBank
copying Bio/GenBank/Scanner.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/GenBank
copying Bio/GenBank/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/GenBank
copying Bio/GenBank/utils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/GenBank
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Geo
copying Bio/Geo/Record.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Geo
copying Bio/Geo/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Geo
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/Comparative.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/Distribution.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics
copying Bio/Graphics/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/GenomeDiagram
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/MarkovModel.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/Trainer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/Utilities.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/HMM
copying Bio/HMM/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/HMM
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG
copying Bio/KEGG/REST.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG
copying Bio/KEGG/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/Compound
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/Enzyme
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/Gene
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/Map
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/mmtfio.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/mmtf
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/KEGG/KGML
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Medline
copying Bio/Medline/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Medline
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/alignace.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/clusterbuster.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/mast.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/matrix.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/meme.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/minimal.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/pfm.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/thresholds.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/transfac.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/motifs/xms.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs/applications
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs/jaspar
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/Nexus.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/Nodes.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/StandardData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/Trees.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/Nexus/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Nexus
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/NMR
copying Bio/NMR/NOEtools.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/NMR
copying Bio/NMR/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/NMR
copying Bio/NMR/xpktools.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/NMR
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Pathway
copying Bio/Pathway/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Pathway
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Pathway/Rep
copying Bio/PDB/AbstractPropertyMap.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Atom.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Chain.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/DSSP.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Dice.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Entity.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/HSExposure.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Model.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/NACCESS.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PDBIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PDBList.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PDBParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PICIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/PSEA.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Polypeptide.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Residue.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/SASA.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/SCADIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Selection.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Structure.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/Superimposer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/cealign.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/ic_data.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/ic_rebuild.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/internal_coords.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/mmcifio.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/qcprot.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/vectors.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/phenotype
copying Bio/phenotype/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/phenotype
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PopGen
copying Bio/PopGen/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PopGen
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PopGen/GenePop
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Restriction
copying Bio/Restriction/Restriction.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Restriction
copying Bio/Restriction/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Restriction
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Cla.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Des.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Dom.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Hie.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Raf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/Residues.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SCOP
copying Bio/SCOP/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SCOP
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/_index.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_legacy
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/_model
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/BlastIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HHsuiteIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/HmmerIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/ExonerateIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SearchIO/InterproscanIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/GckIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/SnapGeneIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/TwoBitIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/XdnaIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/SeqIO/_index.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqUtils
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Sequencing/Applications
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SVDSuperimposer
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SwissProt
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/TogoWS
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/CDAO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/Consensus.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/NeXML.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/Newick.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/_io.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
copying Bio/Phylo/_utils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/Applications
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Phylo/PAML
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/UniGene
copying Bio/UniGene/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/UniGene
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/UniProt
copying Bio/UniProt/GOA.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/UniProt
copying Bio/UniProt/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/UniProt
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Wise
copying Bio/Wise/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Wise
copying Bio/Wise/dnal.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Wise
copying Bio/Wise/psw.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Wise
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/BioSeq.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/BioSeqDatabase.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/DBUtils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/Loader.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/BioSQL
copying BioSQL/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/BioSQL
running egg_info
creating biopython.egg-info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
writing manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'Bio.Align.substitution_matrices.data' as data is deprecated, please list it in `packages`.
    !!


    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'Bio.Align.substitution_matrices.data' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'Bio.Align.substitution_matrices.data' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.


!!

  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'Bio.Entrez.DTDs' as data is deprecated, please list it in `packages`.
    !!


    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'Bio.Entrez.DTDs' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'Bio.Entrez.DTDs' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'Bio.Entrez.DTDs' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.


!!

  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'Bio.Entrez.XSDs' as data is deprecated, please list it in `packages`.
    !!


    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'Bio.Entrez.XSDs' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'Bio.Entrez.XSDs' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'Bio.Entrez.XSDs' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.


!!

  check.warn(importable)
copying Bio/cpairwise2module.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio
copying Bio/Align/_aligners.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER22 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER6 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER74 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTN -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTP -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/FENG -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GENETIC -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/HOXD70 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JOHNSON -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JONES -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/LEVIN -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MDM78 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MEGABLAST -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM250 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM30 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM70 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RAO -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RISLER -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/STR -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/TRANS -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/substitution_matrices/data
copying Bio/Cluster/cluster.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Cluster
copying Bio/Cluster/cluster.h -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Cluster
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-display1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-format1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-link1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-list1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-math1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-para1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-references1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-section1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivearticle.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/articlemeta.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/backmatter.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/chars.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/common.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-classes.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-mixes.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/display.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSearch_020511.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSpell.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSummary_041029.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/egquery.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/einfo.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/elink_020122.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esearch.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/format.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/htmltable.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsa.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsb.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsc.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsn.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamso.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsr.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isobox.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr1.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isodia.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk1.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk4.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat1.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomfrk.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomopf.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomscr.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isonum.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isopub.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isotech.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/journalmeta.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/link.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/list.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/math.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlalias.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlextra.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/modules.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pmc-1.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/taxon.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-table-1.mod -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/DTDs
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs
copying Bio/Nexus/cnexus.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Nexus
copying Bio/PDB/ccealignmodule.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/PDB/kdtrees.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB
copying Bio/SeqIO/_twoBitIO.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer
running build_ext
building 'Bio.Align._aligners' extension
creating build
creating build/temp.linux-armhf-cpython-311
creating build/temp.linux-armhf-cpython-311/Bio
creating build/temp.linux-armhf-cpython-311/Bio/Align
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligners.c -o build/temp.linux-armhf-cpython-311/Bio/Align/_aligners.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/Align/_aligners.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Align/_aligners.cpython-311-arm-linux-gnueabihf.so
building 'Bio.cpairwise2' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-armhf-cpython-311/Bio/cpairwise2module.o
Bio/cpairwise2module.c: In function '_get_match_score':
Bio/cpairwise2module.c:60:5: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
   60 |     if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
      |     ^~
In file included from /usr/include/python3.11/Python.h:95,
                 from Bio/cpairwise2module.c:16:
/usr/include/python3.11/ceval.h:27:43: note: declared here
   27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/cpairwise2module.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/cpairwise2.cpython-311-arm-linux-gnueabihf.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-armhf-cpython-311/Bio/Nexus
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-armhf-cpython-311/Bio/Nexus/cnexus.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Nexus/cnexus.cpython-311-arm-linux-gnueabihf.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-armhf-cpython-311/Bio/PDB
creating build/temp.linux-armhf-cpython-311/Bio/PDB/QCPSuperimposer
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armhf-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-arm-linux-gnueabihf.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-armhf-cpython-311/Bio/motifs
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-armhf-cpython-311/Bio/motifs/_pwm.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/motifs/_pwm.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/motifs/_pwm.cpython-311-arm-linux-gnueabihf.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-armhf-cpython-311/Bio/Cluster
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-armhf-cpython-311/Bio/Cluster/cluster.o
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armhf-cpython-311/Bio/Cluster/clustermodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/Cluster/cluster.o build/temp.linux-armhf-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Cluster/_cluster.cpython-311-arm-linux-gnueabihf.so
building 'Bio.PDB.kdtrees' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-armhf-cpython-311/Bio/PDB/kdtrees.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/kdtrees.cpython-311-arm-linux-gnueabihf.so
building 'Bio.PDB.ccealign' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-armhf-cpython-311/Bio/PDB/ccealignmodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/ccealign.cpython-311-arm-linux-gnueabihf.so
building 'Bio.SeqIO._twoBitIO' extension
creating build/temp.linux-armhf-cpython-311/Bio/SeqIO
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-armhf-cpython-311/Bio/SeqIO/_twoBitIO.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/_twoBitIO.cpython-311-arm-linux-gnueabihf.so
I: pybuild base:240: /usr/bin/python3 setup.py build 
running build
running build_py
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/File.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/LogisticRegression.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/MarkovModel.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/MaxEntropy.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/NaiveBayes.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/Seq.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/SeqFeature.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/SeqRecord.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/_utils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/bgzf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/kNN.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/pairwise2.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Affy
copying Bio/Affy/CelFile.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Affy
copying Bio/Affy/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Affy
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/AlignInfo.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/a2m.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/bed.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/bigbed.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/bigmaf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/bigpsl.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/clustal.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/emboss.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/exonerate.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/fasta.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/hhr.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/interfaces.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/maf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/mauve.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/msf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/nexus.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/phylip.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/psl.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/sam.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/stockholm.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
copying Bio/Align/tabular.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/Applications
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices
copying Bio/Align/substitution_matrices/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/MsfIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/AlignIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Alphabet
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Application
copying Bio/Application/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Application
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast
copying Bio/Blast/Applications.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast
copying Bio/Blast/NCBIXML.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast
copying Bio/Blast/Record.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast
copying Bio/Blast/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Blast
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/CAPS
copying Bio/CAPS/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/CAPS
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster
copying Bio/Cluster/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign
copying Bio/codonalign/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign
copying Bio/codonalign/codonseq.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Compass
copying Bio/Compass/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Compass
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Data
copying Bio/Data/CodonTable.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Data
copying Bio/Data/IUPACData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Data
copying Bio/Data/PDBData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Data
copying Bio/Data/SCOPData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Data
copying Bio/Data/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Data
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss
copying Bio/Emboss/Applications.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss
copying Bio/Emboss/Primer3.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss
copying Bio/Emboss/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Emboss
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez
copying Bio/Entrez/Parser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez
copying Bio/Entrez/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/ExPASy
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank
copying Bio/GenBank/Record.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank
copying Bio/GenBank/Scanner.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank
copying Bio/GenBank/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank
copying Bio/GenBank/utils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Geo
copying Bio/Geo/Record.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Geo
copying Bio/Geo/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Geo
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics
copying Bio/Graphics/Comparative.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics
copying Bio/Graphics/Distribution.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics
copying Bio/Graphics/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Graphics/GenomeDiagram
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM
copying Bio/HMM/MarkovModel.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM
copying Bio/HMM/Trainer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM
copying Bio/HMM/Utilities.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM
copying Bio/HMM/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/HMM
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG
copying Bio/KEGG/REST.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG
copying Bio/KEGG/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Compound
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Enzyme
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Gene
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/Map
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/mmtf
copying Bio/PDB/mmtf/mmtfio.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/mmtf
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/KEGG/KGML
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Medline
copying Bio/Medline/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Medline
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/alignace.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/clusterbuster.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/mast.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/matrix.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/meme.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/minimal.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/pfm.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/thresholds.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/transfac.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/motifs/xms.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/applications
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/jaspar
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus
copying Bio/Nexus/Nexus.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus
copying Bio/Nexus/Nodes.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus
copying Bio/Nexus/StandardData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus
copying Bio/Nexus/Trees.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus
copying Bio/Nexus/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/NMR
copying Bio/NMR/NOEtools.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/NMR
copying Bio/NMR/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/NMR
copying Bio/NMR/xpktools.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/NMR
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway
copying Bio/Pathway/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Pathway/Rep
copying Bio/PDB/AbstractPropertyMap.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Atom.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Chain.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/DSSP.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Dice.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Entity.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/HSExposure.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Model.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/NACCESS.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/PDBIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/PDBList.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/PDBParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/PICIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/PSEA.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Polypeptide.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Residue.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/SASA.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/SCADIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Selection.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Structure.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/Superimposer.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/cealign.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/ic_data.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/ic_rebuild.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/internal_coords.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/mmcifio.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/qcprot.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/vectors.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/phenotype
copying Bio/phenotype/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/phenotype
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen
copying Bio/PopGen/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PopGen/GenePop
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction
copying Bio/Restriction/Restriction.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction
copying Bio/Restriction/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Restriction
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP
copying Bio/SCOP/Cla.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP
copying Bio/SCOP/Des.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP
copying Bio/SCOP/Dom.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP
copying Bio/SCOP/Hie.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP
copying Bio/SCOP/Raf.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP
copying Bio/SCOP/Residues.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP
copying Bio/SCOP/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SCOP
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO
copying Bio/SearchIO/_index.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_legacy
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/_model
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/BlastIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HHsuiteIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/HmmerIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/ExonerateIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SearchIO/InterproscanIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/GckIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/SnapGeneIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/TwoBitIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/XdnaIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/SeqIO/_index.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqUtils
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Sequencing/Applications
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SVDSuperimposer
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/QCPSuperimposer
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SwissProt
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/TogoWS
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/CDAO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/Consensus.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/NeXML.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/Newick.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/_io.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
copying Bio/Phylo/_utils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/Applications
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Phylo/PAML
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/UniGene
copying Bio/UniGene/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/UniGene
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/UniProt
copying Bio/UniProt/GOA.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/UniProt
copying Bio/UniProt/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/UniProt
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Wise
copying Bio/Wise/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Wise
copying Bio/Wise/dnal.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Wise
copying Bio/Wise/psw.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Wise
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/BioSQL
copying BioSQL/BioSeq.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/BioSQL
copying BioSQL/BioSeqDatabase.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/BioSQL
copying BioSQL/DBUtils.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/BioSQL
copying BioSQL/Loader.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/BioSQL
copying BioSQL/__init__.py -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/BioSQL
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'Bio.Align.substitution_matrices.data' as data is deprecated, please list it in `packages`.
    !!


    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'Bio.Align.substitution_matrices.data' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'Bio.Align.substitution_matrices.data' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.


!!

  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'Bio.Entrez.DTDs' as data is deprecated, please list it in `packages`.
    !!


    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'Bio.Entrez.DTDs' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'Bio.Entrez.DTDs' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'Bio.Entrez.DTDs' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.


!!

  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'Bio.Entrez.XSDs' as data is deprecated, please list it in `packages`.
    !!


    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'Bio.Entrez.XSDs' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'Bio.Entrez.XSDs' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'Bio.Entrez.XSDs' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.


!!

  check.warn(importable)
copying Bio/cpairwise2module.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio
copying Bio/Align/_aligners.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER22 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER6 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER74 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTN -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTP -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM45 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM50 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM62 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM80 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM90 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/DAYHOFF -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/FENG -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GENETIC -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GONNET1992 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/HOXD70 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JOHNSON -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JONES -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/LEVIN -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MCLACHLAN -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MDM78 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MEGABLAST -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/NUC.4.4 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM250 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM30 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM70 -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RAO -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RISLER -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/SCHNEIDER -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/STR -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/TRANS -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/substitution_matrices/data
copying Bio/Cluster/cluster.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster
copying Bio/Cluster/cluster.h -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-display1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-format1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-link1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-list1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-math1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-para1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-references1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-section1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivearticle.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/articlemeta.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/backmatter.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/chars.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/common.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-classes.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-mixes.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/display.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSearch_020511.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSpell.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSummary_041029.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/egquery.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/einfo.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/elink_020122.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esearch.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/format.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/htmltable.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsa.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsb.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsc.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsn.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamso.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsr.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isobox.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr1.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isodia.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk1.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk3.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk4.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat1.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat2.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomfrk.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomopf.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomscr.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isonum.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isopub.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isotech.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/journalmeta.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/link.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/list.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/math.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3-qname1.mod -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlalias.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlextra.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/modules.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pmc-1.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180601.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_190101.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/taxon.dtd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-table-1.mod -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/DTDs
creating /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs
copying Bio/Nexus/cnexus.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus
copying Bio/PDB/ccealignmodule.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/PDB/kdtrees.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB
copying Bio/SeqIO/_twoBitIO.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/QCPSuperimposer
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-armhf-cpython-310
creating build/temp.linux-armhf-cpython-310/Bio
creating build/temp.linux-armhf-cpython-310/Bio/Align
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/Align/_aligners.c -o build/temp.linux-armhf-cpython-310/Bio/Align/_aligners.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/Align/_aligners.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Align/_aligners.cpython-310-arm-linux-gnueabihf.so
building 'Bio.cpairwise2' extension
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/cpairwise2module.c -o build/temp.linux-armhf-cpython-310/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/python3.10/Python.h:130,
                 from Bio/cpairwise2module.c:16:
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/cpairwise2module.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/cpairwise2.cpython-310-arm-linux-gnueabihf.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-armhf-cpython-310/Bio/Nexus
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/Nexus/cnexus.c -o build/temp.linux-armhf-cpython-310/Bio/Nexus/cnexus.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/Nexus/cnexus.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Nexus/cnexus.cpython-310-arm-linux-gnueabihf.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-armhf-cpython-310/Bio/PDB
creating build/temp.linux-armhf-cpython-310/Bio/PDB/QCPSuperimposer
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armhf-cpython-310/Bio/PDB/QCPSuperimposer/qcprotmodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-310-arm-linux-gnueabihf.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-armhf-cpython-310/Bio/motifs
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/motifs/_pwm.c -o build/temp.linux-armhf-cpython-310/Bio/motifs/_pwm.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/motifs/_pwm.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/motifs/_pwm.cpython-310-arm-linux-gnueabihf.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-armhf-cpython-310/Bio/Cluster
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/Cluster/cluster.c -o build/temp.linux-armhf-cpython-310/Bio/Cluster/cluster.o
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armhf-cpython-310/Bio/Cluster/clustermodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/Cluster/cluster.o build/temp.linux-armhf-cpython-310/Bio/Cluster/clustermodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Cluster/_cluster.cpython-310-arm-linux-gnueabihf.so
building 'Bio.PDB.kdtrees' extension
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/PDB/kdtrees.c -o build/temp.linux-armhf-cpython-310/Bio/PDB/kdtrees.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/PDB/kdtrees.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/kdtrees.cpython-310-arm-linux-gnueabihf.so
building 'Bio.PDB.ccealign' extension
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-armhf-cpython-310/Bio/PDB/ccealignmodule.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/PDB/ccealignmodule.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/ccealign.cpython-310-arm-linux-gnueabihf.so
building 'Bio.SeqIO._twoBitIO' extension
creating build/temp.linux-armhf-cpython-310/Bio/SeqIO
arm-linux-gnueabihf-gcc -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=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-armhf-cpython-310/Bio/SeqIO/_twoBitIO.o
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-biopython-1.80+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/Bio/SeqIO/_twoBitIO.o -L/usr/lib/arm-linux-gnueabihf -o /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/_twoBitIO.cpython-310-arm-linux-gnueabihf.so
cd Doc && make
make[2]: Entering directory '/<<BUILDDIR>>/python-biopython-1.80+dfsg/Doc'
sed "s/\@VERSION\@/1.80/g" version.in > version.sh
chmod +x version.sh
hevea -exec ./version.sh -exec xxdate.exe -fix Tutorial.tex
Exclude comment 'comment'
./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009'
./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000'
./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_introduction.tex:97: Warning: Undefined citation: 'dehoon2004'
./Tutorial/chapter_introduction.tex:98: Warning: Undefined citation: 'pritchard2006'
./Tutorial/chapter_introduction.tex:99: Warning: Undefined citation: 'talevich2012'
./Tutorial/chapter_introduction.tex:100: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_introduction.tex:185: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_introduction.tex:191: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced'
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined label: 'sec:connecting-with-biological-databases'
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_quick_start.tex:150: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_quick_start.tex:158: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_quick_start.tex:159: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined label: 'sec:mutable-seq'
./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_objects.tex:157: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_seq_objects.tex:353: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seq_objects.tex:475: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:33: Warning: Undefined label: 'sec:FASTQ-filtering-example'
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:600: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_seq_annot.tex:793: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_annot.tex:805: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer'
./Tutorial/chapter_seq_annot.tex:806: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor'
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seqio.tex:14: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:SeqIO_Online'
./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:43: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_seqio.tex:68: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab'
./Tutorial/chapter_seqio.tex:150: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:306: Warning: Undefined label: 'sec:writing-sequence-files'
./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:329: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:398: Warning: Undefined label: 'sec:SeqIO-index-bgzf'
./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:414: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:509: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_seqio.tex:565: Warning: Undefined label: 'sec:seqio_todict'
./Tutorial/chapter_seqio.tex:571: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:575: Warning: Undefined label: 'sec:SeqIO-index-db'
./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-indexing-discussion'
./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:661: Warning: Undefined label: 'sec:fasta-parsing'
./Tutorial/chapter_seqio.tex:783: Warning: Undefined label: 'sec:fastq-indexing'
./Tutorial/chapter_seqio.tex:804: Warning: Undefined label: 'sec:seqio-todict-functionkey'
./Tutorial/chapter_seqio.tex:866: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_seqio.tex:948: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fastq-conversion'
./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion'
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined label: 'sec:seq-reverse-complement'
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_seqio.tex:1311: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seqio.tex:1412: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_align.tex:31: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument'
./Tutorial/chapter_align.tex:113: Warning: Undefined label: 'sec:alignment-format'
./Tutorial/chapter_align.tex:444: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_align.tex:633: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_align.tex:813: Warning: Undefined label: 'sec:SeqRecord-addition'
./Tutorial/chapter_align.tex:892: Warning: Undefined label: 'sec:subs_mat_ex'
./Tutorial/chapter_align.tex:913: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_align.tex:917: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_align.tex:947: Warning: Undefined label: 'sec:emboss-needle-water'
./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:1093: Warning: Undefined label: 'chapter:phylo'
./Tutorial/chapter_align.tex:1317: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:1492: Warning: Undefined citation: 'durbin1998'
./Tutorial/chapter_align.tex:1505: Warning: Undefined label: 'sec:pairwise-aligner'
./Tutorial/chapter_align.tex:1578: Warning: Undefined citation: 'waterman1987'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-substitution-scores'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1609: Warning: Undefined label: 'sec:pairwise-basic'
./Tutorial/chapter_align.tex:1612: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1613: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1639: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1639: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1668: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1772: Warning: Undefined label: 'table:align-meta-attributes'
./Tutorial/chapter_align.tex:1908: Warning: Undefined label: 'sec:pairwise-examples'
./Tutorial/chapter_align.tex:2424: Warning: Undefined citation: 'kent2002'
./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2725: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:2725: Warning: Undefined label: 'sec:substitution_matrices'
./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:3282: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'henikoff1992'
./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'dayhoff1978'
./Tutorial/chapter_align.tex:3379: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:3379: Warning: Suppressing nested a element
./Tutorial/chapter_align.tex:3391: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio'
./Tutorial/chapter_blast.tex:73: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:133: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:138: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:160: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:169: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:178: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:206: Warning: Undefined label: 'sec:alignment-tools'
./Tutorial/chapter_blast.tex:241: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:287: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:289: Warning: Undefined label: 'sec:running-local-blast'
./Tutorial/chapter_blast.tex:304: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_blast.tex:452: Warning: Undefined label: 'fig:blastrecord'
./Tutorial/chapter_blast.tex:468: Warning: Undefined label: 'fig:psiblastrecord'
./Tutorial/chapter_searchio.tex:739: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_searchio.tex:1089: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_entrez.tex:21: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:60: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:63: Warning: Undefined label: 'sec:BioSQL'
./Tutorial/chapter_entrez.tex:216: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:220: Warning: Undefined label: 'sec:entrez-einfo'
./Tutorial/chapter_entrez.tex:236: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:299: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:419: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:481: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:483: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:565: Warning: Undefined label: 'sec:elink-citations'
./Tutorial/chapter_entrez.tex:571: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:780: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:780: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:902: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1065: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1068: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1072: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1115: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1161: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1216: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1251: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1258: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:1259: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:1335: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_entrez.tex:1336: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1396: Warning: Undefined label: 'sec:entrez-search-fetch-genbank'
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:1507: Warning: Undefined label: 'sec:entrez-and-medline'
./Tutorial/chapter_entrez.tex:1512: Warning: Undefined label: 'sec:elink'
./Tutorial/chapter_entrez.tex:1537: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt'
./Tutorial/chapter_uniprot.tex:37: Warning: Undefined label: 'sec:expasy_swissprot'
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt'
./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:345: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_pdb.tex:84: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:275: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:284: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:421: Warning: Undefined label: 'sec:hetero_problems'
./Tutorial/chapter_pdb.tex:466: Warning: Undefined label: 'sec:point_mutations'
./Tutorial/chapter_pdb.tex:483: Warning: Undefined label: 'sec:disordered_atoms'
./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:610: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:657: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:973: Warning: Undefined label: 'table:ic-attribs'
./Tutorial/chapter_pdb.tex:1018: Warning: Undefined citation: 'golub1989'
./Tutorial/chapter_pdb.tex:1046: Warning: Undefined citation: 'hamelryck2005'
./Tutorial/chapter_pdb.tex:1081: Warning: Undefined label: 'table:DSSP-codes'
./Tutorial/chapter_pdb.tex:1121: Warning: Undefined label: 'sec:residue_depth'
./Tutorial/chapter_pdb.tex:1124: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1172: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_pdb.tex:1186: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1383: Warning: Undefined citation: 'hamelryck2003b'
./Tutorial/chapter_pdb.tex:1384: Warning: Undefined citation: 'majumdar2005'
./Tutorial/chapter_phylo.tex:9: Warning: Undefined citation: 'talevich2012'
./Tutorial/chapter_phylo.tex:96: Warning: Undefined label: 'fig:phylo-simple-draw'
./Tutorial/chapter_phylo.tex:201: Warning: Undefined label: 'fig:phylo-color-draw'
./Tutorial/chapter_phylo.tex:823: Warning: Undefined label: 'sec:PhyloXML'
./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links'
./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cornish1985'
./Tutorial/chapter_motifs.tex:166: Warning: Undefined citation: 'cavener1987'
./Tutorial/chapter_motifs.tex:542: Warning: Undefined citation: 'bailey1994'
./Tutorial/chapter_motifs.tex:688: Warning: Undefined citation: 'matys2003'
./Tutorial/chapter_motifs.tex:772: Warning: Undefined label: 'table:transfaccodes'
./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004'
./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988'
./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988'
./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989'
./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:278: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:346: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:556: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'kohonen1997'
./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'tamayo1999'
./Tutorial/chapter_cluster.tex:647: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:660: Warning: Undefined citation: 'yeung2001'
./Tutorial/chapter_cluster.tex:668: Warning: Undefined citation: 'golub1971'
./Tutorial/chapter_cluster.tex:802: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:805: Warning: Undefined label: 'sec:distancematrix'
./Tutorial/chapter_cluster.tex:823: Warning: Undefined label: 'sec:clustercentroids'
./Tutorial/chapter_cluster.tex:846: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:871: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:900: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:922: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:954: Warning: Undefined citation: 'hihara2001'
./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'sec:LogisticRegression'
./Tutorial/chapter_learning.tex:277: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegressionTraining'
./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006'
./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006'
./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009'
./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:345: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down'
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002'
./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002'
./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012'
./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:206: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_cookbook.tex:338: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_cookbook.tex:443: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:457: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_cookbook.tex:643: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:646: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_cookbook.tex:801: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:823: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:825: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:1024: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:1418: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1436: Warning: Undefined label: 'sec:consensus'
./Tutorial/chapter_cookbook.tex:1437: Warning: Undefined label: 'sec:pssm'
./Tutorial/chapter_cookbook.tex:1438: Warning: Undefined label: 'sec:getting_info_content'
./Tutorial/chapter_cookbook.tex:1439: Warning: Undefined label: 'sec:sub_matrix'
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1640: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_testing.tex:55: Warning: Undefined label: 'sec:doctest'
./Tutorial/chapter_testing.tex:282: Warning: Undefined label: 'sec:doctest'
./Tutorial/chapter_contributing.tex:32: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex: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_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced'
./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:3379: Warning: Suppressing nested a element
./Tutorial/chapter_entrez.tex:1065: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1068: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1124: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1186: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode
Fixpoint reached in 2 step(s)
hevea -exec ./version.sh -exec xxdate.exe -fix -text Tutorial.tex
Exclude comment 'comment'
./Tutorial.tex:73: Warning: tt_mode is an empty style
./Tutorial.tex:100: Warning: Application of '\'' on 'n' failed
./Tutorial.htoc:378: Warning: Application of '\"' on 'i' failed
./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced'
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:84: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:118: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:296: Warning: Command not found: \downarrow
./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:120: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:139: Warning: line too long
./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:197: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:218: Warning: line too long
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:508: Warning: line too long
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:668: Warning: line too long
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: line too long
./Tutorial/chapter_seq_annot.tex:704: Warning: line too long
./Tutorial/chapter_seq_annot.tex:704: Warning: line too long
./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:715: Warning: line too long
./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:725: Warning: line too long
./Tutorial/chapter_seq_annot.tex:746: Warning: line too long
./Tutorial/chapter_seq_annot.tex:746: Warning: line too long
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:880: Warning: line too long
./Tutorial/chapter_seq_annot.tex:897: Warning: line too long
./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1: Warning: line too long
./Tutorial/chapter_seqio.tex:1: Warning: line too long
./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:150: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:248: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:550: Warning: line too long
./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:850: Warning: line too long
./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1818: Warning: overfull line in array : array too wide
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2295: Warning: line too long
./Tutorial/chapter_align.tex:2311: Warning: line too long
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2428: Warning: line too long
./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3448: Warning: line too long
./Tutorial/chapter_align.tex:3450: Warning: line too long
./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:1: Warning: line too long
./Tutorial/chapter_blast.tex:1: Warning: line too long
./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:45: Warning: line too long
./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:440: Warning: line too long
./Tutorial/chapter_blast.tex:442: Warning: line too long
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:456: Warning: Image in text
./Tutorial/chapter_blast.tex:472: Warning: Image in text
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1: Warning: line too long
./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:29: Warning: '_' occurring outside math mode
./Tutorial/chapter_searchio.tex:31: Warning: '_' occurring outside math mode
./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:733: Warning: line too long
./Tutorial/chapter_searchio.tex:735: Warning: line too long
./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:966: Warning: line too long
./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:909: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:909: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:949: Warning: line too long
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1047: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1047: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1051: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1051: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1065: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1068: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:1: Warning: line too long
./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:31: Warning: line too long
./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:497: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:1: Warning: line too long
./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:288: Warning: Image in text
./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:995: Warning: overfull line in array : array too wide
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:1124: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1186: Warning: '_' occurring outside math mode
./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:107: Warning: Image in text
./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:208: Warning: Image in text
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:388: Warning: line too long
./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:401: Warning: Image in text
./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1: Warning: line too long
./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:550: Warning: line too long
./Tutorial/chapter_motifs.tex:552: Warning: line too long
./Tutorial/chapter_motifs.tex:558: Warning: line too long
./Tutorial/chapter_motifs.tex:560: Warning: line too long
./Tutorial/chapter_motifs.tex:569: Warning: line too long
./Tutorial/chapter_motifs.tex:573: Warning: line too long
./Tutorial/chapter_motifs.tex:575: Warning: line too long
./Tutorial/chapter_motifs.tex:584: Warning: line too long
./Tutorial/chapter_motifs.tex:586: Warning: line too long
./Tutorial/chapter_motifs.tex:587: Warning: line too long
./Tutorial/chapter_motifs.tex:589: Warning: line too long
./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1567: Warning: '_' occurring outside math mode
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:112: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cluster.tex:115: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:607: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:611: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:616: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:711: Warning: line too long
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:749: Warning: overfull line in array : array too wide
./Tutorial/chapter_cluster.tex:749: Warning: line too long
./Tutorial/chapter_cluster.tex:749: Warning: line too long
./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:26: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_learning.tex:36: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"]
./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"]
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_learning.tex:70: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:397: Warning: Application of '\"' on 'i' failed
./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:68: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:132: Warning: Image in text
./Tutorial/chapter_graphics.tex:132: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:163: Warning: Image in text
./Tutorial/chapter_graphics.tex:163: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:325: Warning: Image in text
./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:396: Warning: Image in text
./Tutorial/chapter_graphics.tex:396: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: Image in text
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: Image in text
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:564: Warning: Image in text
./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:566: Warning: Image in text
./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:728: Warning: Image in text
./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:890: Warning: Image in text
./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:923: Warning: Image in text
./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1035: Warning: line too long
./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1110: Warning: Image in text
./Tutorial/chapter_graphics.tex:1110: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:1125: Warning: line too long
./Tutorial/chapter_graphics.tex:1190: Warning: Image in text
./Tutorial/chapter_graphics.tex:1190: Warning: '_' occurring outside math mode
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:10: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:452: Warning: line too long
./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:561: Warning: line too long
./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:804: Warning: line too long
./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:904: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1053: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1094: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1094: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1127: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1163: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1163: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1211: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1265: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1265: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1341: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1363: Warning: line too long
./Tutorial/chapter_cookbook.tex:1364: Warning: line too long
./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1412: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1743: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:222: Warning: line too long
./Tutorial/chapter_testing.tex:275: Warning: line too long
./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:11: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex: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:126: Warning: line too long
./Tutorial.tex:137: Warning: Application of '\'' on 'e' failed
./Tutorial.tex:137: Warning: Application of '\'' on 'o' failed
./Tutorial.tex:141: Warning: Application of '\"' on 'u' failed
./Tutorial.tex:215: Warning: Application of '\"' on 'o' failed
./Tutorial.tex:215: Warning: Application of '\"' on 'u' failed
HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right.
Run, run, again...
Exclude comment 'comment'
./Tutorial.tex:73: Warning: tt_mode is an empty style
./Tutorial.haux:561: Giving up command: \@hevea@cbrace
./Tutorial.tex:73: Giving up command: \input
./Tutorial.tex:73: Warning: Failure while reading .haux
./Tutorial.tex:100: Warning: Application of '\'' on 'n' failed
./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:91: Warning: Undefined citation: 'cock2009'
./Tutorial/chapter_introduction.tex:95: Warning: Undefined citation: 'chapman2000'
./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:96: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:97: Warning: Undefined citation: 'dehoon2004'
./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:98: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:98: Warning: Undefined citation: 'pritchard2006'
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:99: Warning: Undefined citation: 'talevich2012'
./Tutorial/chapter_introduction.tex:100: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:152: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:185: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:191: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:222: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:226: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:229: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:231: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_introduction.tex:232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced'
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:33: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:45: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_quick_start.tex:65: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:72: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:74: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:79: Warning: Undefined label: 'sec:connecting-with-biological-databases'
./Tutorial/chapter_quick_start.tex:84: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:118: Warning: '_' occurring outside math mode
./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:150: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_quick_start.tex:158: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_quick_start.tex:159: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:160: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_quick_start.tex:169: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:1: Warning: line too long
./Tutorial/chapter_seq_objects.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:9: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined label: 'sec:mutable-seq'
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:133: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:155: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:156: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:157: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:278: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:296: Warning: Command not found: \downarrow
./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:305: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:353: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:470: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:475: Warning: Undefined label: 'sec:seq-module-functions'
./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:598: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:641: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:702: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:741: Warning: Undefined label: 'sec:seq-to-string'
./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_objects.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:2: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:20: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:33: Warning: Undefined label: 'sec:FASTQ-filtering-example'
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:37: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:47: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:52: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:99: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:112: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:120: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:130: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:132: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:139: Warning: line too long
./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:142: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:143: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:197: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:211: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:218: Warning: line too long
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:227: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:275: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_seq_annot.tex:278: Warning: '_' occurring outside math mode
./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:284: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:292: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:293: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:298: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:320: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:327: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:380: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:383: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:472: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:502: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:508: Warning: line too long
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:522: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:548: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:568: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:600: Warning: Undefined label: 'sec:seq-comparison'
./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:606: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:608: Warning: Undefined label: 'sec:locations'
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:610: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:647: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:648: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:649: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:651: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:668: Warning: line too long
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:683: Warning: line too long
./Tutorial/chapter_seq_annot.tex:704: Warning: line too long
./Tutorial/chapter_seq_annot.tex:704: Warning: line too long
./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:715: Warning: line too long
./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:725: Warning: line too long
./Tutorial/chapter_seq_annot.tex:746: Warning: line too long
./Tutorial/chapter_seq_annot.tex:746: Warning: line too long
./Tutorial/chapter_seq_annot.tex:793: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seq_annot.tex:805: Warning: Undefined label: 'sec:FASTQ-slicing-off-primer'
./Tutorial/chapter_seq_annot.tex:806: Warning: Undefined label: 'sec:FASTQ-slicing-off-adaptor'
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:880: Warning: line too long
./Tutorial/chapter_seq_annot.tex:897: Warning: line too long
./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:916: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:939: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seq_annot.tex:956: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1: Warning: line too long
./Tutorial/chapter_seqio.tex:1: Warning: line too long
./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:quick_start'
./Tutorial/chapter_seqio.tex:4: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:12: Warning: Undefined label: 'chapter:seq_objects'
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:14: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:SeqIO_Online'
./Tutorial/chapter_seqio.tex:22: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:28: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:43: Warning: Undefined label: 'sec:sequence-parsing'
./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:43: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:54: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:67: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:68: Warning: Undefined label: 'sec:sequence-parsing-plus-pylab'
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:149: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:150: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_seqio.tex:150: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:248: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:290: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:291: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:306: Warning: Undefined label: 'sec:writing-sequence-files'
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:309: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:329: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:398: Warning: Undefined label: 'sec:SeqIO-index-bgzf'
./Tutorial/chapter_seqio.tex:401: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:413: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:414: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:471: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'chapter:entrez'
./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:504: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:509: Warning: Undefined label: 'chapter:uniprot'
./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:540: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:550: Warning: line too long
./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:560: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:564: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:565: Warning: Undefined label: 'sec:seqio_todict'
./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:567: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:569: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:570: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:571: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:575: Warning: Undefined label: 'sec:SeqIO-index-db'
./Tutorial/chapter_seqio.tex:578: Warning: Undefined label: 'sec:SeqIO-indexing-discussion'
./Tutorial/chapter_seqio.tex:581: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:588: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:602: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:605: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined label: 'sec:fasta-parsing'
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:661: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:663: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:676: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:742: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:783: Warning: Undefined label: 'sec:fastq-indexing'
./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:804: Warning: Undefined label: 'sec:seqio-todict-functionkey'
./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:850: Warning: line too long
./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:851: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:866: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:879: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:947: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:948: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:976: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:978: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:979: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:982: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1026: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1034: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1038: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1039: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1062: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1073: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1080: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1196: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1198: Warning: '_' occurring outside math mode
./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fastq-conversion'
./Tutorial/chapter_seqio.tex:1232: Warning: Undefined label: 'sec:SeqIO-fasta-qual-conversion'
./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1247: Warning: Undefined label: 'sec:seq-reverse-complement'
./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1258: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_seqio.tex:1311: Warning: Undefined label: 'sec:SeqIO-translate'
./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1331: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1364: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1367: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_seqio.tex:1412: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:1: Warning: line too long
./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:13: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:24: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:31: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:35: Warning: Undefined label: 'sec:AlignIO-count-argument'
./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:93: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:113: Warning: Undefined label: 'sec:alignment-format'
./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:368: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:370: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:374: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:376: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:444: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:467: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:614: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:631: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined label: 'sec:SeqRecord-format'
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:664: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:665: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:666: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:687: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:688: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:813: Warning: Undefined label: 'sec:SeqRecord-addition'
./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:892: Warning: Undefined label: 'sec:subs_mat_ex'
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:894: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:913: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:917: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:933: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:947: Warning: Undefined label: 'sec:emboss-needle-water'
./Tutorial/chapter_align.tex:955: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1016: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1048: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1050: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1069: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1093: Warning: Undefined label: 'chapter:phylo'
./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1098: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1161: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1317: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1377: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1457: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1487: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1492: Warning: Undefined citation: 'durbin1998'
./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1505: Warning: Undefined label: 'sec:pairwise-aligner'
./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1554: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1556: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1558: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1578: Warning: Undefined citation: 'waterman1987'
./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-substitution-scores'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1608: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined label: 'sec:pairwise-basic'
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1612: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1613: Warning: Undefined label: 'sec:pairwise-general-gapscores'
./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined label: 'sec:pairwise-affine-gapscores'
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1707: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1708: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1709: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1722: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1729: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1730: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1731: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1732: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1733: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1734: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1772: Warning: Undefined label: 'table:align-meta-attributes'
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1802: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1804: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1805: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1806: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1807: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1808: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1809: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1818: Warning: overfull line in array : array too wide
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1818: Warning: line too long
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1863: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1908: Warning: Undefined label: 'sec:pairwise-examples'
./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1912: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1984: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1988: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1989: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:1999: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2053: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2054: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2067: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2091: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2164: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2192: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2295: Warning: line too long
./Tutorial/chapter_align.tex:2311: Warning: line too long
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2366: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2379: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2411: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2412: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2424: Warning: Undefined citation: 'kent2002'
./Tutorial/chapter_align.tex:2428: Warning: line too long
./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2437: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2479: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2485: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2493: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2496: Warning: Multiple definitions for label: sec:pairwise-general-gapscores
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2498: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2698: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2721: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2725: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:2725: Warning: Undefined label: 'sec:substitution_matrices'
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2864: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2932: Warning: '_' occurring outside math mode
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2934: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2938: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2951: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2958: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2975: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:2993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3007: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3049: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3070: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3072: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3107: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3232: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3282: Warning: Undefined citation: 'altschul1990'
./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3282: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'henikoff1992'
./Tutorial/chapter_align.tex:3354: Warning: Undefined citation: 'dayhoff1978'
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3379: Warning: Undefined citation: 'schneider2005'
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3391: Warning: Undefined label: 'sec:pairwise'
./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3393: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3396: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3429: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3448: Warning: line too long
./Tutorial/chapter_align.tex:3450: Warning: line too long
./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3508: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3529: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_align.tex:3572: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:1: Warning: line too long
./Tutorial/chapter_blast.tex:1: Warning: line too long
./Tutorial/chapter_blast.tex:18: Warning: Undefined label: 'chapter:searchio'
./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:20: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:29: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:45: Warning: line too long
./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:65: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:69: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:71: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:73: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:133: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:138: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:147: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:157: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:159: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:160: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:169: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:178: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:202: Warning: '_' occurring outside math mode
./Tutorial/chapter_blast.tex:206: Warning: Undefined label: 'sec:alignment-tools'
./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:241: Warning: Undefined label: 'sec:parsing-blast'
./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:287: Warning: Undefined label: 'sec:running-www-blast'
./Tutorial/chapter_blast.tex:289: Warning: Undefined label: 'sec:running-local-blast'
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:303: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:304: Warning: Undefined label: 'sec:appendix-handles'
./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:307: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:339: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_blast.tex:340: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:440: Warning: line too long
./Tutorial/chapter_blast.tex:442: Warning: line too long
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:450: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:452: Warning: Undefined label: 'fig:blastrecord'
./Tutorial/chapter_blast.tex:456: Warning: Image in text
./Tutorial/chapter_blast.tex:468: Warning: Undefined label: 'fig:psiblastrecord'
./Tutorial/chapter_blast.tex:472: Warning: Image in text
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:489: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:494: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:502: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_blast.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1: Warning: line too long
./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:18: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:21: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:29: Warning: '_' occurring outside math mode
./Tutorial/chapter_searchio.tex:31: Warning: '_' occurring outside math mode
./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:32: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:40: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:42: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:44: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:46: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:72: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:79: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:81: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:83: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:84: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:87: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:88: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:97: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:100: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:103: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:244: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:315: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:360: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:361: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:388: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:394: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:406: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:410: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:413: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:414: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:416: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:443: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:444: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:468: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:469: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:475: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:476: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:477: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:506: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:557: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:561: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:562: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:563: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:577: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:590: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:615: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:616: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:618: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:622: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:627: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:630: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:633: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:656: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:700: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:705: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:727: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:733: Warning: line too long
./Tutorial/chapter_searchio.tex:735: Warning: line too long
./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:738: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:739: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:740: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:741: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:744: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:756: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:850: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:853: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:878: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:881: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:883: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:884: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:885: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:904: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:910: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:922: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:923: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:966: Warning: line too long
./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:973: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:983: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:996: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1003: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1009: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1010: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1014: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1015: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1023: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1024: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1027: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1030: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1032: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1035: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1055: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1058: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1083: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1084: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1088: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1089: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1090: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1119: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1132: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1139: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1140: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1141: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1155: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1163: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1165: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_searchio.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:1: Warning: line too long
./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:7: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:15: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:17: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:21: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:38: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:60: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:63: Warning: Undefined label: 'sec:BioSQL'
./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:78: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:135: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:171: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:200: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:216: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:220: Warning: Undefined label: 'sec:entrez-einfo'
./Tutorial/chapter_entrez.tex:236: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:259: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:299: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:323: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:325: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:325: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:441: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:481: Warning: Undefined label: 'sec:entrez-specialized-parsers'
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:483: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:565: Warning: Undefined label: 'sec:elink-citations'
./Tutorial/chapter_entrez.tex:571: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:573: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:591: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:609: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:611: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:619: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:660: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:750: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:778: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:780: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:780: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:837: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:852: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:902: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:909: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:909: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:949: Warning: line too long
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:991: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:993: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1000: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1008: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1022: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1029: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1045: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1046: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1047: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1047: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1051: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1051: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1065: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1068: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1072: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1086: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1115: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1159: Warning: '_' occurring outside math mode
./Tutorial/chapter_entrez.tex:1161: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_entrez.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1190: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1216: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1251: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1258: Warning: Undefined label: 'sec:SeqIO_GenBank_Online'
./Tutorial/chapter_entrez.tex:1259: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1311: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_entrez.tex:1335: Warning: Undefined label: 'sec:entrez-guidelines'
./Tutorial/chapter_entrez.tex:1336: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_entrez.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1396: Warning: Undefined label: 'sec:entrez-search-fetch-genbank'
./Tutorial/chapter_entrez.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1405: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined label: 'sec:entrez_example_genbank'
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1440: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1507: Warning: Undefined label: 'sec:entrez-and-medline'
./Tutorial/chapter_entrez.tex:1507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_entrez.tex:1512: Warning: Undefined label: 'sec:elink'
./Tutorial/chapter_entrez.tex:1537: Warning: Undefined label: 'sec:entrez-webenv'
./Tutorial/chapter_uniprot.tex:1: Warning: line too long
./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt'
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:31: Warning: line too long
./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:37: Warning: Undefined label: 'sec:expasy_swissprot'
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined label: 'sec:SeqIO_ExPASy_and_SwissProt'
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:53: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:77: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:80: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:80: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:82: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:191: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:249: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:251: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:286: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:316: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:340: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:343: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:345: Warning: Undefined label: 'sec:orchids'
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:381: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:446: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:448: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:466: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:497: Warning: '_' occurring outside math mode
./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_uniprot.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:1: Warning: line too long
./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:25: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:84: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:86: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:113: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:122: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:203: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:204: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:275: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:284: Warning: Undefined label: 'sec:problem_structures'
./Tutorial/chapter_pdb.tex:288: Warning: Image in text
./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:350: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:351: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:353: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:363: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:421: Warning: Undefined label: 'sec:hetero_problems'
./Tutorial/chapter_pdb.tex:466: Warning: Undefined label: 'sec:point_mutations'
./Tutorial/chapter_pdb.tex:483: Warning: Undefined label: 'sec:disordered_atoms'
./Tutorial/chapter_pdb.tex:592: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:606: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:610: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:646: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:657: Warning: Undefined label: 'fig:smcra'
./Tutorial/chapter_pdb.tex:683: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:760: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_pdb.tex:973: Warning: Undefined label: 'table:ic-attribs'
./Tutorial/chapter_pdb.tex:995: Warning: overfull line in array : array too wide
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:995: Warning: line too long
./Tutorial/chapter_pdb.tex:1018: Warning: Undefined citation: 'golub1989'
./Tutorial/chapter_pdb.tex:1046: Warning: Undefined citation: 'hamelryck2005'
./Tutorial/chapter_pdb.tex:1081: Warning: Undefined label: 'table:DSSP-codes'
./Tutorial/chapter_pdb.tex:1121: Warning: Undefined label: 'sec:residue_depth'
./Tutorial/chapter_pdb.tex:1124: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1172: Warning: Undefined citation: 'hamelryck2003a'
./Tutorial/chapter_pdb.tex:1186: Warning: '_' occurring outside math mode
./Tutorial/chapter_pdb.tex:1383: Warning: Undefined citation: 'hamelryck2003b'
./Tutorial/chapter_pdb.tex:1384: Warning: Undefined citation: 'majumdar2005'
./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_popgen.tex:19: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:9: Warning: Undefined citation: 'talevich2012'
./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:70: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:96: Warning: Undefined label: 'fig:phylo-simple-draw'
./Tutorial/chapter_phylo.tex:107: Warning: Image in text
./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:123: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:183: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:194: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:201: Warning: Undefined label: 'fig:phylo-color-draw'
./Tutorial/chapter_phylo.tex:208: Warning: Image in text
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:343: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:375: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:388: Warning: line too long
./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:392: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:401: Warning: Image in text
./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:418: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:424: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:427: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:428: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:430: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:431: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:432: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:434: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:435: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:452: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:462: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:483: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:510: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:523: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:524: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:526: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:535: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:549: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:586: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:612: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:613: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:617: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:648: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:669: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:673: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:701: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:719: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:720: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phylo.tex:823: Warning: Undefined label: 'sec:PhyloXML'
./Tutorial/chapter_motifs.tex:1: Warning: line too long
./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:8: Warning: Undefined label: 'sec:links'
./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:11: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:12: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:14: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:27: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:36: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:85: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:138: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:146: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:165: Warning: Undefined citation: 'cornish1985'
./Tutorial/chapter_motifs.tex:166: Warning: Undefined citation: 'cavener1987'
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:210: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:211: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:213: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:215: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:216: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:217: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:218: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:220: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:224: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:230: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:248: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:257: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:304: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:306: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:426: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:455: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:481: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:501: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:503: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:542: Warning: Undefined citation: 'bailey1994'
./Tutorial/chapter_motifs.tex:550: Warning: line too long
./Tutorial/chapter_motifs.tex:552: Warning: line too long
./Tutorial/chapter_motifs.tex:558: Warning: line too long
./Tutorial/chapter_motifs.tex:560: Warning: line too long
./Tutorial/chapter_motifs.tex:569: Warning: line too long
./Tutorial/chapter_motifs.tex:573: Warning: line too long
./Tutorial/chapter_motifs.tex:575: Warning: line too long
./Tutorial/chapter_motifs.tex:584: Warning: line too long
./Tutorial/chapter_motifs.tex:586: Warning: line too long
./Tutorial/chapter_motifs.tex:587: Warning: line too long
./Tutorial/chapter_motifs.tex:589: Warning: line too long
./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:603: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:604: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:620: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:621: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:657: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:688: Warning: Undefined citation: 'matys2003'
./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:710: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:712: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:743: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:747: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:749: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:757: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:772: Warning: Undefined label: 'table:transfaccodes'
./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:781: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:784: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:786: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:787: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:788: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:790: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:791: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:792: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:793: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:794: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:795: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:797: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:798: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:803: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:810: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:811: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:812: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:813: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:814: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:882: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:908: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:960: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:974: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:987: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1025: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1044: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1065: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1082: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1093: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1102: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1109: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1110: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1169: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1214: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1446: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1465: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1492: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1497: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1504: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1530: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1532: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1533: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1534: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_motifs.tex:1565: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1566: Warning: '_' occurring outside math mode
./Tutorial/chapter_motifs.tex:1567: Warning: '_' occurring outside math mode
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:6: Warning: Undefined citation: 'dehoon2004'
./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:8: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:26: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'lecuyer1988'
./Tutorial/chapter_cluster.tex:30: Warning: Undefined citation: 'kachitvichyanukul1988'
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:37: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:39: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:41: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:43: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:45: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:47: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:49: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:51: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:76: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:84: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:86: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:112: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cluster.tex:115: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'x' failed
./Tutorial/chapter_cluster.tex:117: Warning: Application of '\=' on 'y' failed
./Tutorial/chapter_cluster.tex:154: Warning: Undefined citation: 'snedecor1989'
./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:162: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:167: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:174: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:176: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:177: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:178: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:179: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:180: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:181: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:182: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:183: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:225: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:233: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:235: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:236: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:237: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:238: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:239: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:240: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:241: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:245: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:258: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:260: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:261: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:262: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:264: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:265: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:266: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:268: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:272: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:274: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:275: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:278: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:281: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:288: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:328: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:331: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:332: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:336: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:338: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:341: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:342: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:344: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:345: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:346: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:347: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:348: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:349: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:352: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:356: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:365: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:382: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:384: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:385: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:386: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:387: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:390: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:417: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:419: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:420: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:421: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:423: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:436: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:447: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:449: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:463: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:474: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:488: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:507: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:509: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:515: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:519: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:521: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:525: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:527: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:531: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:539: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:541: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:542: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:543: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:544: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:545: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:546: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:547: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:550: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:551: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:552: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:553: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:555: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:556: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:559: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:566: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:583: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:587: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:588: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:589: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:594: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:596: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'kohonen1997'
./Tutorial/chapter_cluster.tex:600: Warning: Undefined citation: 'tamayo1999'
./Tutorial/chapter_cluster.tex:607: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:611: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:616: Warning: Cannot output that numerical entity: U+00B7
./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:623: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:625: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:632: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:634: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:635: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:636: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:637: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:638: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:639: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:640: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:643: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:646: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:647: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:650: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:652: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:654: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:655: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:660: Warning: Undefined citation: 'yeung2001'
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined citation: 'golub1971'
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:668: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:670: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:677: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:678: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:679: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:680: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:681: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:683: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:686: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:690: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:692: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:711: Warning: line too long
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:716: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:749: Warning: overfull line in array : array too wide
./Tutorial/chapter_cluster.tex:749: Warning: line too long
./Tutorial/chapter_cluster.tex:749: Warning: line too long
./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:755: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:758: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:761: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:762: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:767: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:768: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:770: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:771: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:773: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:774: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:776: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:779: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:780: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:782: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:783: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:785: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:789: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:800: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:801: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:802: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:805: Warning: Undefined label: 'sec:distancematrix'
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:815: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:816: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:817: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:818: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:819: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:820: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:823: Warning: Undefined label: 'sec:clustercentroids'
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:832: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:833: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:834: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:835: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:836: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:840: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:842: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:843: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:845: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:846: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:847: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:848: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:849: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:860: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:861: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:862: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:865: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:866: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:867: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:868: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:870: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:871: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:872: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:886: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:888: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:889: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:890: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:891: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:892: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:895: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:896: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:898: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:899: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:900: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:903: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:913: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:917: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:918: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:919: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:921: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:922: Warning: Undefined label: 'sec:distancefunctions'
./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:925: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:927: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:929: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:930: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:941: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:942: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:943: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:944: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:945: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:946: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:949: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:952: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:954: Warning: Undefined citation: 'hihara2001'
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:971: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cluster.tex:986: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:26: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:28: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_learning.tex:36: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"]
./Tutorial/chapter_learning.tex:37: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber-valign"]
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:39: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:39: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:40: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:70: Warning: overfull line in array : array too wide
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:70: Warning: line too long
./Tutorial/chapter_learning.tex:75: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:104: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:166: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:168: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:172: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:197: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:261: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:OP'
./Tutorial/chapter_learning.tex:263: Warning: Undefined label: 'eq:NOP'
./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:273: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:273: Warning: Undefined label: 'sec:LogisticRegression'
./Tutorial/chapter_learning.tex:277: Warning: Undefined label: 'table:training'
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined label: 'sec:LogisticRegressionTraining'
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:289: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:302: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:397: Warning: Application of '\"' on 'i' failed
./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:399: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_learning.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:4: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:16: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006'
./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006'
./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009'
./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:35: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seq_annot'
./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:63: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_graphics.tex:68: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:89: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:90: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:106: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:132: Warning: Image in text
./Tutorial/chapter_graphics.tex:132: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:144: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:163: Warning: Image in text
./Tutorial/chapter_graphics.tex:163: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:217: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:219: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:220: Warning: Undefined label: 'sec:seq_features'
./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:221: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:223: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:268: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:271: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:277: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:279: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:325: Warning: Image in text
./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:325: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:326: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:345: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_graphics.tex:352: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:396: Warning: Image in text
./Tutorial/chapter_graphics.tex:396: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:409: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: Image in text
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:430: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: Image in text
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:459: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:473: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:482: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:485: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:488: Warning: Undefined label: 'sec:gd_top_down'
./Tutorial/chapter_graphics.tex:564: Warning: Image in text
./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:564: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:566: Warning: Image in text
./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:566: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:591: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:596: Warning: Undefined citation: 'proux2002'
./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:599: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:600: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:601: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:605: Warning: Undefined label: 'sec:efetch'
./Tutorial/chapter_graphics.tex:608: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_graphics.tex:610: Warning: Undefined label: 'sec:SeqRecord-reverse-complement'
./Tutorial/chapter_graphics.tex:728: Warning: Image in text
./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:728: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:752: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:759: Warning: Undefined citation: 'proux2002'
./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:841: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:843: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:873: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:874: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:875: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:876: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:890: Warning: Image in text
./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:890: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:914: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:917: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:923: Warning: Image in text
./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:923: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:953: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:954: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1004: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1006: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1011: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1012: Warning: Undefined citation: 'jupe2012'
./Tutorial/chapter_graphics.tex:1035: Warning: line too long
./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1036: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1057: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_graphics.tex:1110: Warning: Image in text
./Tutorial/chapter_graphics.tex:1110: Warning: '_' occurring outside math mode
./Tutorial/chapter_graphics.tex:1125: Warning: line too long
./Tutorial/chapter_graphics.tex:1190: Warning: Image in text
./Tutorial/chapter_graphics.tex:1190: Warning: '_' occurring outside math mode
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:1: Warning: line too long
./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:10: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_kegg.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:10: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:30: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode
./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_phenotype.tex:235: Warning: Optional argument to \item in itemize environment
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:1: Warning: line too long
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:55: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:60: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:105: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:115: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:116: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:125: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:126: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO'
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:202: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:205: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:206: Warning: Undefined label: 'sec:SeqIO-reverse-complement'
./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:207: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:208: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:243: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:252: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:253: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:263: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:267: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:280: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:283: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:310: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:326: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:329: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:330: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:333: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:334: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:335: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:337: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:338: Warning: Undefined label: 'sec:seqio-index-getraw'
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:357: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:359: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:439: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:442: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:443: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:452: Warning: line too long
./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:454: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:456: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:457: Warning: Undefined label: 'sec:low-level-fasta-fastq'
./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:459: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:460: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:461: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:480: Warning: Undefined label: 'sec:SeqRecord-slicing'
./Tutorial/chapter_cookbook.tex:561: Warning: line too long
./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:593: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:595: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:643: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:644: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:646: Warning: Undefined citation: 'cock2010'
./Tutorial/chapter_cookbook.tex:655: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:657: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:675: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:686: Warning: Undefined block in text mode: 'DIV' [class="equationcontainer"]
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' [class="equationnumber"]
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'SPAN' []
./Tutorial/chapter_cookbook.tex:688: Warning: Undefined block in text mode: 'DIV' []
./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:694: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:695: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:714: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:715: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:759: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:764: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:766: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:777: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:796: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:799: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:801: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:804: Warning: line too long
./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:821: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:823: Warning: Undefined label: 'sec:SeqIO-index'
./Tutorial/chapter_cookbook.tex:825: Warning: Undefined label: 'sec:SeqIO-sort'
./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:826: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:839: Warning: Undefined label: 'sec:SeqIO-conversion'
./Tutorial/chapter_cookbook.tex:904: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:905: Warning: Undefined label: 'sec:translation'
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:915: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1024: Warning: Undefined label: 'sec:gd_nice_example'
./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1031: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1041: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1042: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1053: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1056: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1094: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1094: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1117: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1118: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1127: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1129: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1163: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1163: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1211: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1242: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1265: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1265: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1285: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1287: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1308: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1341: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1341: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1363: Warning: line too long
./Tutorial/chapter_cookbook.tex:1364: Warning: line too long
./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1369: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1391: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1397: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1398: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1412: Warning: Image in text
./Tutorial/chapter_cookbook.tex:1418: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1421: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1425: Warning: Undefined label: 'chapter:align'
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1433: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1436: Warning: Undefined label: 'sec:consensus'
./Tutorial/chapter_cookbook.tex:1437: Warning: Undefined label: 'sec:pssm'
./Tutorial/chapter_cookbook.tex:1438: Warning: Undefined label: 'sec:getting_info_content'
./Tutorial/chapter_cookbook.tex:1439: Warning: Undefined label: 'sec:sub_matrix'
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1445: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1451: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1453: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1484: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1491: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1511: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1513: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1528: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1538: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1565: Warning: Undefined label: 'sec:summary_info'
./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1571: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1582: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1584: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1592: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1617: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1626: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1640: Warning: Undefined label: 'sec:align_clustal'
./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1642: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1703: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1743: Warning: '_' occurring outside math mode
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_cookbook.tex:1748: Warning: Undefined label: 'chapter:seqio'
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:1: Warning: line too long
./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:5: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:22: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:23: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:34: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:48: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:55: Warning: Undefined label: 'sec:doctest'
./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:62: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:68: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:73: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:74: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:75: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:111: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:114: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:120: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:121: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:127: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:145: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:150: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:154: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:187: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:189: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:193: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:195: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:197: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:198: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:201: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:212: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:222: Warning: line too long
./Tutorial/chapter_testing.tex:275: Warning: line too long
./Tutorial/chapter_testing.tex:282: Warning: Undefined label: 'sec:doctest'
./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:284: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:297: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:301: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:311: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:313: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:318: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:319: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:354: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:355: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:371: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:373: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:389: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:400: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:401: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:402: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:403: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:404: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:407: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:408: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_testing.tex:409: Warning: Undefined block in text mode: 'CODE' []
./Tutorial/chapter_contributing.tex:11: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex:32: Warning: Undefined label: 'chapter:cookbook'
./Tutorial/chapter_contributing.tex:38: Warning: '_' occurring outside math mode
./Tutorial/chapter_contributing.tex: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:126: Warning: line too long
./Tutorial.tex:137: Warning: Application of '\'' on 'e' failed
./Tutorial.tex:137: Warning: Application of '\'' on 'o' failed
./Tutorial.tex:141: Warning: Application of '\"' on 'u' failed
./Tutorial.tex:215: Warning: Application of '\"' on 'o' failed
./Tutorial.tex:215: Warning: Application of '\"' on 'u' failed
Fixpoint reached in 2 step(s)
pdflatex --shell-escape "\def\bpversion{1.80}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2022-11-01>
L3 programming layer <2022-11-02> (./Tutorial.tex
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2022/07/02 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty)
(/usr/share/texmf/tex/latex/misc/hevea.sty
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') Excluding comment 'rawhtml'
Excluding comment 'htmlonly')
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/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/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

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

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

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

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

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


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


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


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


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


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


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

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


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

(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/C3217FD04973F24516F5530BB525A22C9D788471CB66B7D26E11C71E228
489B2.pygtex) [4 <./images/biopython_logo_old.jpg>]

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


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

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

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

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


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


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


(./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612C9D788471CB66B7D26E11C71E228
489B2.pygtex [7])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535AB9D788471CB66B7D26E11C71E228
489B2.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/AD9EF2BC42CEF4E413923F9BFFE1BE07EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B02133467818559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26D9D788471CB66B7D26E11C71E228
489B2.pygtex [9])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F29D788471CB66B7D26E11C71E228
489B2.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/048D805D0CE39D0271B0A9A9F6FA0B909D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDC9D788471CB66B7D26E11C71E228
489B2.pygtex) [12]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0F44B540F3531194878FC29AF0179029D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A49D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E976225049D788471CB66B7D26E11C71E228
489B2.pygtex [13])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D93864209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79A9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/732D927996C79742AC990312B3D6EEB09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C2709D788471CB66B7D26E11C71E228
489B2.pygtex [14])
(./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC479D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D3949D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8D9D788471CB66B7D26E11C71E228
489B2.pygtex [15])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF179D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC09D788471CB66B7D26E11C71E228
489B2.pygtex [16])
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C87539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B3869D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A709D788471CB66B7D26E11C71E228
489B2.pygtex [17])
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD649D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF989D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE799D788471CB66B7D26E11C71E228
489B2.pygtex [18])
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B559909D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874D9D788471CB66B7D26E11C71E228
489B2.pygtex [19])
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/06DBC59F2EAD33E7A9518885378766159D788471CB66B7D26E11C71E228
489B2.pygtex) [20]
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE69D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C3389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CBEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [21])
(./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E849D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DFDB859800920408E228736AD921B5DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B0409D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE4519D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2E9D788471CB66B7D26E11C71E228
489B2.pygtex [22])
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CB9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C09D788471CB66B7D26E11C71E228
489B2.pygtex)) [23] [24] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

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


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


(./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC8099D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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



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

[25]

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


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



(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D4079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC29D788471CB66B7D26E11C71E228
489B2.pygtex [26])
(./_minted-Tutorial/510764EE0BB38AD6C688E71989677507EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)

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


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


(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D8498229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD20859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [27])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4AEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)

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


(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA6019D788471CB66B7D26E11C71E228
489B2.pygtex [28])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F9269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0D9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


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

[29] [30]
(./_minted-Tutorial/AD47AD29D6F7927F9406BE56096763889D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F39D788471CB66B7D26E11C71E228
489B2.pygtex [31])
(./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A19D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/D86C559003980DC8749AF92530435DFD9D788471CB66B7D26E11C71E228
489B2.pygtex) [32]
(./_minted-Tutorial/1C0A562378DEEE8E210765437B3E17009D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B499D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0C3ED75879971F09D72A92585654A32C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E39209D788471CB66B7D26E11C71E228
489B2.pygtex [33])
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312D9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F96899D788471CB66B7D26E11C71E228
489B2.pygtex [34])

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


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


(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B23409D788471CB66B7D26E11C71E228
489B2.pygtex [35])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEB9D788471CB66B7D26E11C71E228
489B2.pygtex) [36]
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B3119D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D24579D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF829D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


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


(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDF9D788471CB66B7D26E11C71E228
489B2.pygtex [37])
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF17185016699D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3E9D788471CB66B7D26E11C71E228
489B2.pygtex [38])
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B639D788471CB66B7D26E11C71E228
489B2.pygtex [39])
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B87939D788471CB66B7D26E11C71E228
489B2.pygtex)) [40] (./Tutorial/chapter_seqio.tex
Chapter 5.

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


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


(./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D4989D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


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


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


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


(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB678D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [41])

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


(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE500954D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB219D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F1D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [42])
(./_minted-Tutorial/C82398A4A04383A063D2E64881123052D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AEDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [43]

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


(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD162221D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD82D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE69D788471CB66B7D26E11C71E228
489B2.pygtex [44])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E73451D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9562C263804C6DD613F075A435553A9F9D788471CB66B7D26E11C71E228
489B2.pygtex [45])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C919D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579D9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/23394A4616015FFE4619934E984241789D788471CB66B7D26E11C71E228
489B2.pygtex [46])
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C099D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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

[47]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD476D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD8D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [48])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)

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


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


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


(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A4D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989F9D788471CB66B7D26E11C71E228
489B2.pygtex [49])

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


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


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


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


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


(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF69D788471CB66B7D26E11C71E228
489B2.pygtex [50])
(./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528FEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)

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


(./_minted-Tutorial/55430EAFE498E385842834603E0B8C86D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB8D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [51])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C1788939D788471CB66B7D26E11C71E228
489B2.pygtex) [52]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF40659D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A3649D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D66D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE9D788471CB66B7D26E11C71E228
489B2.pygtex [53])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853
\OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org /
 pub / databases / uniprot / current _ release / knowledgebase / complete /

(./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929D9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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

(./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C141CFBAB8D39E8FFAF3C5D885168
6F649.pygtex [54])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41041CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A27779D788471CB66B7D26E11C71E228
489B2.pygtex) [55]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C64719D788471CB66B7D26E11C71E228
489B2.pygtex) [56]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD7342D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [57])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [58])

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


(./_minted-Tutorial/C194E2231D844AE7D0223173D2A89991D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEA9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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

[59]

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


(./_minted-Tutorial/920133226A22EEB682D854077D7FB78F9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C2600289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E381FF526AC999B71717F178C997F6B29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26A9D788471CB66B7D26E11C71E228
489B2.pygtex)

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

[60]
(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EAD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

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


(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F53D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351
\OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) 
[]\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm
tt/m/n/10 SeqRecord.format(...)
[61]
(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397
[]\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm
tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt
/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D39D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/D749A84299CF58E876E9A899069830DBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)) [62] (./Tutorial/chapter_align.tex
Chapter 6.

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


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


(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [63])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AEC9D788471CB66B7D26E11C71E228
489B2.pygtex [64])

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


(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A310779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [65]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C5604079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [66])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF7569D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DEEF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [67]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [68])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [69]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D3189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [70])
Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435
\OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t
or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()

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


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

(./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F40249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479FEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [71])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [72])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F16D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [73])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE69D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/2590B11C695B984E246A0A91734F786C9D788471CB66B7D26E11C71E228
489B2.pygtex) [74]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE59D788471CB66B7D26E11C71E228
489B2.pygtex [75])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B716929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB009D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E599D788471CB66B7D26E11C71E228
489B2.pygtex [76])

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


(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A92539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AE857C14E4731CC6F6EBA530514600979D788471CB66B7D26E11C71E228
489B2.pygtex) [77]
(./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239C9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/523928538FA511A925EC995B1803BD169D788471CB66B7D26E11C71E228
489B2.pygtex)

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


[78]

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


(./_minted-Tutorial/CD47D1913C82182C164BD47DA47152829D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E8939D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C630649D788471CB66B7D26E11C71E228
489B2.pygtex) [79]
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A4429D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F9863689D788471CB66B7D26E11C71E228
489B2.pygtex [80])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDF9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B0459D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B274259D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130
[]\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi
le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO

(./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BD9D788471CB66B7D26E11C71E228
489B2.pygtex [81])
(./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F7399989D788471CB66B7D26E11C71E228
489B2.pygtex [82])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E74549D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C9D788471CB66B7D26E11C71E228
489B2.pygtex [83])
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE749D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A2409D788471CB66B7D26E11C71E228
489B2.pygtex) [84]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/39152F199CEBB3375366F2E9478245199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF3856749D788471CB66B7D26E11C71E228
489B2.pygtex [85])
(./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE24939D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DF151703751D72BD556402B910190A879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA889D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/554024580088332FAF0EA9296BACE82E9D788471CB66B7D26E11C71E228
489B2.pygtex)

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

[86]
(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E3619D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6CCC707502EDD92E9C355854215BF8859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C59D788471CB66B7D26E11C71E228
489B2.pygtex [87])

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



(./_minted-Tutorial/E5E00F47BD7A0C8BC5F88185262838689D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


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


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


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


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


(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE049D788471CB66B7D26E11C71E228
489B2.pygtex) [88]

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



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


(./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD59D788471CB66B7D26E11C71E228
489B2.pygtex)

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



(./_minted-Tutorial/48453D528762FF183499778647AF218B9D788471CB66B7D26E11C71E228
489B2.pygtex [89])
(./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A399D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix
 []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu
tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt
t/m/n/10 aligner.mismatch_score

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

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


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


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

(./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CE9D788471CB66B7D26E11C71E228
489B2.pygtex [90]) [91] [92]
(./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514A9D788471CB66B7D26E11C71E228
489B2.pygtex)

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

[93]
(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE19119D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB86719D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EF9D788471CB66B7D26E11C71E228
489B2.pygtex [94])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D019D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9F9D788471CB66B7D26E11C71E228
489B2.pygtex [95])
(./_minted-Tutorial/0758643069FF669538B9540ECD26C94C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A342965929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/76E331C5187C259B69198E91FC4AD1129D788471CB66B7D26E11C71E228
489B2.pygtex [96])
(./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD3579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966B9D788471CB66B7D26E11C71E228
489B2.pygtex [97])
(./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/66AABFA387595237A8CE2518915213F89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B15E737F9393063B641148640673D9919D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B469D788471CB66B7D26E11C71E228
489B2.pygtex [98])
(./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/874975627BAB24A36A35FD4C633D246D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BD9D788471CB66B7D26E11C71E228
489B2.pygtex [99])
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A79D788471CB66B7D26E11C71E228
489B2.pygtex [100])
(./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/52868B2F44504455E4969FEF2614B63B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB949D788471CB66B7D26E11C71E228
489B2.pygtex) [101]
(./_minted-Tutorial/E7E68A8851DEEE300947A0531513417D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF659D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA17339D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/6502BA65433924876427DBB6013C10039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FD9D788471CB66B7D26E11C71E228
489B2.pygtex [102])
(./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F10129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA50779D788471CB66B7D26E11C71E228
489B2.pygtex [103])
(./_minted-Tutorial/779C61444C54C1736794F4E11B0E326D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E1059D788471CB66B7D26E11C71E228
489B2.pygtex [104])
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF7966009D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613
\OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments 
is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing
 [][]\OT1/cmtt/m/n/10 len(alignments)

(./_minted-Tutorial/F89522EF58FB067C6521C367C71347169D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9C9D788471CB66B7D26E11C71E228
489B2.pygtex [105])
(./_minted-Tutorial/882BD2544386DECA236BF25C7DD648579D788471CB66B7D26E11C71E228
489B2.pygtex [106])
(./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA709D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A299D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/13D646E6B49807044DBDC43707A098469D788471CB66B7D26E11C71E228
489B2.pygtex [107])
(./_minted-Tutorial/467CA50C36874E405E988587FEC076869D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E629D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A94C18D2207C354646F831D57FD85B359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D89D788471CB66B7D26E11C71E228
489B2.pygtex [108])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A739D788471CB66B7D26E11C71E228
489B2.pygtex [109])
(./_minted-Tutorial/AAF53200644F4F68779FB844730087D39D788471CB66B7D26E11C71E228
489B2.pygtex [110])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057D9D788471CB66B7D26E11C71E228
489B2.pygtex [111])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BAB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/842D73F66680850822D006857AE71FE79D788471CB66B7D26E11C71E228
489B2.pygtex) [112]
(./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE31359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7C466424D72F09AE5AACA884161416F99D788471CB66B7D26E11C71E228
489B2.pygtex [113])
(./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA8252789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F6800939D788471CB66B7D26E11C71E228
489B2.pygtex [114])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315EC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D862416647079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [115])
(./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/60D893638743BD147116D13E00593D6C9D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [116])
(./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9ED9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6D9D788471CB66B7D26E11C71E228
489B2.pygtex [117])

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


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



(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE99D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F25199D788471CB66B7D26E11C71E228
489B2.pygtex)

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

(/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED09D788471CB66B7D26E11C71E228
489B2.pygtex) [118]
(./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F120EF3444F3192D48657B4E524070179D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F20919D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5D9D788471CB66B7D26E11C71E228
489B2.pygtex [119])
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C719D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A9D788471CB66B7D26E11C71E228
489B2.pygtex [120])) [121] (./Tutorial/chapter_blast.tex
Chapter 7.

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


Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46
[]\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas
t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs 
&
[122]
(./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB19D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4E9D788471CB66B7D26E11C71E228
489B2.pygtex [123])

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


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


(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC69D788471CB66B7D26E11C71E228
489B2.pygtex)

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


(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C2049D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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

[124]

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


(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE47929D788471CB66B7D26E11C71E228
489B2.pygtex)

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

[125]

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


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


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


(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C2049D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE52180049D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F403949D788471CB66B7D26E11C71E228
489B2.pygtex [126])
(./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D2389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68259DF5B1930070C029D5A72D891A369D788471CB66B7D26E11C71E228
489B2.pygtex [127])
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)

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

Excluding 'htmlonly' comment.

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

Excluding 'htmlonly' comment.

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

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

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [131]
Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93
[][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle 
con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10
 HSPFragment

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

(./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FC9D788471CB66B7D26E11C71E228
489B2.pygtex [132])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B519559D788471CB66B7D26E11C71E228
489B2.pygtex [133])
(./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/362861C831165FEA5413E0240053CD899D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE3279D788471CB66B7D26E11C71E228
489B2.pygtex [134])
(./_minted-Tutorial/FD9C81C098491598DBFB6208173BB5759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A039D788471CB66B7D26E11C71E228
489B2.pygtex) [135]
(./_minted-Tutorial/0B914838010D3E86EC368E1702EB72539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E6199D788471CB66B7D26E11C71E228
489B2.pygtex [136])
(./_minted-Tutorial/DDECA9EB99D9FA38003A52C1765930729D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/578CBF904F35965EECFEC1FA694F07529D788471CB66B7D26E11C71E228
489B2.pygtex [137])
(./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD649D788471CB66B7D26E11C71E228
489B2.pygtex) [138]
(./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC62468639D788471CB66B7D26E11C71E228
489B2.pygtex) [139]
(./_minted-Tutorial/A3385B945E43CC076FFA693B27681F059D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE5735779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B469D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD959D788471CB66B7D26E11C71E228
489B2.pygtex [140])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD8804449D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C7879D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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

(./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A35369099D788471CB66B7D26E11C71E228
489B2.pygtex [141])
(./_minted-Tutorial/16771935702D6A2A9762A80A621013D89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/046FE550C51B323D1E952A27E126FE199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A55E467518B2E0F936A232F0970B10379D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB20219D788471CB66B7D26E11C71E228
489B2.pygtex [142])
(./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EED9D788471CB66B7D26E11C71E228
489B2.pygtex [143])
(./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D339D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/758BAC7574A59544686354199D20892C9D788471CB66B7D26E11C71E228
489B2.pygtex) [144]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA99D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059
\OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT
1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like 
[][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F49D788471CB66B7D26E11C71E228
489B2.pygtex) [145]

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


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

(./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E98689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DE9D788471CB66B7D26E11C71E228
489B2.pygtex) [146]
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170
[]\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 
also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic
h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse

(./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C1769D788471CB66B7D26E11C71E228
489B2.pygtex)) [147] (./Tutorial/chapter_entrez.tex
Chapter 9.
[148]

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


(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB59D788471CB66B7D26E11C71E228
489B2.pygtex) [149]

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


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


(./_minted-Tutorial/7692669934D8ED6DEE1B8B66847454219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA369D788471CB66B7D26E11C71E228
489B2.pygtex [150])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C0089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FAC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F69D788471CB66B7D26E11C71E228
489B2.pygtex [151])
(./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C689D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D502779D788471CB66B7D26E11C71E228
489B2.pygtex)

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

[152]
(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19F9D788471CB66B7D26E11C71E228
489B2.pygtex)

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

[153]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE49D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F31479D788471CB66B7D26E11C71E228
489B2.pygtex [154] [155])

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


(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [156])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F4879D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF0089D788471CB66B7D26E11C71E228
489B2.pygtex [157])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68622353B578A611D2F621023E3C4BD19D788471CB66B7D26E11C71E228
489B2.pygtex)

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


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


(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F709D788471CB66B7D26E11C71E228
489B2.pygtex [158])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0941CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722A9D788471CB66B7D26E11C71E228
489B2.pygtex [159])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF38EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [160]
(./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1BEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [161])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB99D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 162 undefined on in
put line 780.


LaTeX Warning: Reference `sec:efetch' on page 162 undefined on input line 780.

[162]
(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AADEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC39D788471CB66B7D26E11C71E228
489B2.pygtex [163])
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E2779D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 164 undefined on input lin
e 902.

[164]
(./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A12669D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [165])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B6249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE19D788471CB66B7D26E11C71E228
489B2.pygtex) [166]
(./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA1D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 167 undefined on input line 1072
.


(./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71A9D788471CB66B7D26E11C71E228
489B2.pygtex [167])
(./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1E9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 168 undefined on input lin
e 1115.


(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD09D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 168 undefined on input line 1161
.

[168]
(./_minted-Tutorial/964257041BEB9E732FF9A943209BD6ED9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/600193D5D5D44162E61A3CAB404484269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B6420389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A09D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 169 undefined on input lin
e 1216.


(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C59D788471CB66B7D26E11C71E228
489B2.pygtex [169])
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A19D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 170 undefined on input lin
e 1251.


LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 170 undefined on in
put line 1258.


LaTeX Warning: Reference `sec:entrez-webenv' on page 170 undefined on input lin
e 1259.


(./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2F9D788471CB66B7D26E11C71E228
489B2.pygtex [170])
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A727979D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB38489D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 171 undefined on input line 13
11.


(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D76169664531538D144C55FFC33571B9D788471CB66B7D26E11C71E228
489B2.pygtex [171])

LaTeX Warning: Reference `sec:entrez-guidelines' on page 172 undefined on input
 line 1335.


LaTeX Warning: Reference `sec:entrez-webenv' on page 172 undefined on input lin
e 1336.


(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C459D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB936499D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D89D788471CB66B7D26E11C71E228
489B2.pygtex) [172]

LaTeX Warning: Reference `sec:entrez-search-fetch-genbank' on page 173 undefine
d on input line 1396.


(./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C4779D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:entrez_example_genbank' on page 173 undefined on 
input line 1418.


(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F96339D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D574D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [173])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFAD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [174])

LaTeX Warning: Reference `sec:entrez-and-medline' on page 175 undefined on inpu
t line 1507.


LaTeX Warning: Reference `sec:elink' on page 175 undefined on input line 1512.


(./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB29D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:entrez-webenv' on page 175 undefined on input lin
e 1537.


(./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927A9D788471CB66B7D26E11C71E228
489B2.pygtex)) [175] (./Tutorial/chapter_uniprot.tex
Chapter 10.

LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 176 undefined
 on input line 12.


(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A869D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A6689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD67689D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:expasy_swissprot' on page 176 undefined on input 
line 37.


(./_minted-Tutorial/930B60BD569CAAF368B0E614553F30309D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 176 undefined
 on input line 45.

[176]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA65191829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB9346699D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD692289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D149D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C069D788471CB66B7D26E11C71E228
489B2.pygtex [177])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A45179189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09AB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [178])
(./_minted-Tutorial/956383F4066B9E093C9D2E3843CA02209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307B9D788471CB66B7D26E11C71E228
489B2.pygtex [179])
(./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E29D788471CB66B7D26E11C71E228
489B2.pygtex) [180]
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5BEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC7839D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF99D788471CB66B7D26E11C71E228
489B2.pygtex [181])
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B49D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:orchids' on page 182 undefined on input line 345.



(./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B6229D788471CB66B7D26E11C71E228
489B2.pygtex [182])
Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366
[]\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n
/10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/
m/n/10 SwissProt.read(handle)

(./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87D9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410
[]\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m
en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re
cord

(./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B7539D788471CB66B7D26E11C71E228
489B2.pygtex) [183]
(./_minted-Tutorial/9457A436D281E066D350873A88476E599D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E79D788471CB66B7D26E11C71E228
489B2.pygtex [184])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E861699D788471CB66B7D26E11C71E228
489B2.pygtex)) [185] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C228539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E690859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C719D788471CB66B7D26E11C71E228
489B2.pygtex [186])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA73889D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB82319D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:problem_structures' on page 187 undefined on inpu
t line 84.


(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879E9D788471CB66B7D26E11C71E228
489B2.pygtex) [187]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D1769D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A0249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A59D788471CB66B7D26E11C71E228
489B2.pygtex) [188]
(./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB1369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECEC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA49D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264
\OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m
/n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato
m)
[189]

LaTeX Warning: Reference `fig:smcra' on page 190 undefined on input line 275.


LaTeX Warning: Reference `sec:problem_structures' on page 190 undefined on inpu
t line 284.

Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D9799D788471CB66B7D26E11C71E228
489B2.pygtex) [190] [191 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD8559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB2479D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E27276229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A129D788471CB66B7D26E11C71E228
489B2.pygtex) [192]

LaTeX Warning: Reference `sec:hetero_problems' on page 193 undefined on input l
ine 421.


(./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E39D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:point_mutations' on page 193 undefined on input l
ine 466.


(./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DC9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:disordered_atoms' on page 193 undefined on input 
line 483.

[193]
(./_minted-Tutorial/35E34E333445AAAA4E33570211335BA59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B19D788471CB66B7D26E11C71E228
489B2.pygtex [194])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC880989D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB124929D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `fig:smcra' on page 195 undefined on input line 610.


(./_minted-Tutorial/76657140082404C594EE786B642215C39D788471CB66B7D26E11C71E228
489B2.pygtex [195])

LaTeX Warning: Reference `fig:smcra' on page 196 undefined on input line 657.


(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254C9D788471CB66B7D26E11C71E228
489B2.pygtex) [196]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB909D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B1289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B39D788471CB66B7D26E11C71E228
489B2.pygtex [197])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF2318999D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A6249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC26639D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA399D788471CB66B7D26E11C71E228
489B2.pygtex [198])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E6679D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899B9D788471CB66B7D26E11C71E228
489B2.pygtex [199])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B33389074760A02AC27316E67DAAB0739D788471CB66B7D26E11C71E228
489B2.pygtex [200])
Overfull \hbox (42.26714pt too wide) in paragraph at lines 956--960
\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 201 undefined on input line
 973.


Overfull \hbox (3.8904pt too wide) in paragraph at lines 976--996
[][] 
[201]

LaTeX Warning: Citation `golub1989' on page 202 undefined on input line 1018.


(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993C9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Citation `hamelryck2005' on page 202 undefined on input line 104
6.


LaTeX Warning: Command \r invalid in math mode on input line 1049.


(./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705E9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `table:DSSP-codes' on page 202 undefined on input line
 1081.


LaTeX Warning: Reference `sec:residue_depth' on page 202 undefined on input lin
e 1121.

[202]
(./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C67099D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/895E3343902EFB0E5475667B01C4B6919D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Citation `hamelryck2003a' on page 203 undefined on input line 11
72.

[203] [204]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A749D788471CB66B7D26E11C71E228
489B2.pygtex [205])
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5D9D788471CB66B7D26E11C71E228
489B2.pygtex) [206]

LaTeX Warning: Citation `hamelryck2003b' on page 207 undefined on input line 13
83.


LaTeX Warning: Citation `majumdar2005' on page 207 undefined on input line 1384
.

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

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [208]
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)) [209] (./Tutorial/chapter_phylo.tex
Chapter 13.

LaTeX Warning: Citation `talevich2012' on page 210 undefined on input line 9.


(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15841CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4AD9D788471CB66B7D26E11C71E228
489B2.pygtex [210])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DD9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `fig:phylo-simple-draw' on page 211 undefined on input
 line 96.


(./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B99D788471CB66B7D26E11C71E228
489B2.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA9D788471CB66B7D26E11C71E228
489B2.pygtex) [211]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185
[]\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t
he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor

(./_minted-Tutorial/29624A9666C9430AABADF395148BBF279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `fig:phylo-color-draw' on page 212 undefined on input 
line 201.


(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B99D788471CB66B7D26E11C71E228
489B2.pygtex [212 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9B9D788471CB66B7D26E11C71E228
489B2.pygtex [213 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/456F5679DCD4FF740E7A110889D865739D788471CB66B7D26E11C71E228
489B2.pygtex [214])
(./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D39D788471CB66B7D26E11C71E228
489B2.pygtex [215])
(./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEE9D788471CB66B7D26E11C71E228
489B2.pygtex) Excluding 'htmlonly' comment. [216 <./images/phylo-draw-example.p
ng>]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486
\OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, 
[][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"})
[217]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537
[]\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, 
find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10
 ,
[218]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF6D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [219]
Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707
[]\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter
-act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier .

(./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD81199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095B9D788471CB66B7D26E11C71E228
489B2.pygtex) [220]
(./_minted-Tutorial/0702C9875263768417DD3ED2EF78755E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D29D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:PhyloXML' on page 221 undefined on input line 823
.

[221]) [222] (./Tutorial/chapter_motifs.tex
Chapter 14.

LaTeX Warning: Reference `sec:links' on page 223 undefined on input line 8.


(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486A9D788471CB66B7D26E11C71E228
489B2.pygtex [223])
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D1779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D2571739D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/86717C2BCE65F41FCDB86527631658579D788471CB66B7D26E11C71E228
489B2.pygtex [224])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F612431920229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F219D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Citation `cornish1985' on page 225 undefined on input line 165.


LaTeX Warning: Citation `cavener1987' on page 225 undefined on input line 166.


(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB24769D788471CB66B7D26E11C71E228
489B2.pygtex) [225]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [226])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECD9D788471CB66B7D26E11C71E228
489B2.pygtex [227])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C769D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [228])
(./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F7069D788471CB66B7D26E11C71E228
489B2.pygtex [229])
(./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DC9D788471CB66B7D26E11C71E228
489B2.pygtex [230])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFD9D788471CB66B7D26E11C71E228
489B2.pygtex [231])
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C3789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6B9D788471CB66B7D26E11C71E228
489B2.pygtex [232])

LaTeX Warning: Citation `bailey1994' on page 233 undefined on input line 542.


(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6ABEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [233])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909F9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606
\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man
d reads the com-plete file di-rectly, so you can close the file af-ter call-ing
 [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B849D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB69D788471CB66B7D26E11C71E228
489B2.pygtex [234])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E0120539D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Citation `matys2003' on page 235 undefined on input line 688.


(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [235])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5C9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `table:transfaccodes' on page 236 undefined on input l
ine 772.


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

[236]
(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EF9D788471CB66B7D26E11C71E228
489B2.pygtex [237])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F264069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF514959D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE706059D788471CB66B7D26E11C71E228
489B2.pygtex [238])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C749D788471CB66B7D26E11C71E228
489B2.pygtex [239])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C988129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E2259D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E489D788471CB66B7D26E11C71E228
489B2.pygtex [240])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7B9D788471CB66B7D26E11C71E228
489B2.pygtex [241])
(./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A819D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA1619D788471CB66B7D26E11C71E228
489B2.pygtex) [242]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E259D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A50929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C860739D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE9709D788471CB66B7D26E11C71E228
489B2.pygtex [243])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF49D788471CB66B7D26E11C71E228
489B2.pygtex [244])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E3229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD72616039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA24739D788471CB66B7D26E11C71E228
489B2.pygtex [245])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA169D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D39D788471CB66B7D26E11C71E228
489B2.pygtex) [246]
(./_minted-Tutorial/868ABF9ABD2736A12F423306646D77069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/912C817861E626118AB2FA06F12910B69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [247]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB419D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B69D788471CB66B7D26E11C71E228
489B2.pygtex) [248]) [249] (./Tutorial/chapter_cluster.tex
Chapter 15.

LaTeX Warning: Citation `dehoon2004' on page 250 undefined on input line 6.


LaTeX Warning: Citation `lecuyer1988' on page 250 undefined on input line 30.


LaTeX Warning: Citation `kachitvichyanukul1988' on page 250 undefined on input 
line 30.

[250] [251] [252]

LaTeX Warning: Citation `snedecor1989' on page 253 undefined on input line 154.


[253]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED41409D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 254 undefined on input
 line 183.


(./_minted-Tutorial/C2B72A7408C7DF74DFCEBE04859972879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE6017358279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A2500D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C09D788471CB66B7D26E11C71E228
489B2.pygtex [254])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246
\OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra
nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$

(./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB349D788471CB66B7D26E11C71E228
489B2.pygtex) [255]

LaTeX Warning: Reference `sec:distancefunctions' on page 256 undefined on input
 line 278.

[256]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E9D788471CB66B7D26E11C71E228
489B2.pygtex) [257]

LaTeX Warning: Reference `sec:distancefunctions' on page 258 undefined on input
 line 346.


(./_minted-Tutorial/C286E2777B917B774560CBDC7CF926269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED18D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7ACD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [258] [259]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424
[][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them.
 The items be-ing clus-tered are num-bered from 0 to $[]$,

(./_minted-Tutorial/015798D317E9D8732518AFD186C997CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C2390492678617399D788471CB66B7D26E11C71E228
489B2.pygtex) [260]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE229D788471CB66B7D26E11C71E228
489B2.pygtex) [261]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F729D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D419D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF88950559D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 262 undefined on input
 line 556.


(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEB9D788471CB66B7D26E11C71E228
489B2.pygtex [262])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED18D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7ACD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Citation `kohonen1997' on page 263 undefined on input line 600.


LaTeX Warning: Citation `tamayo1999' on page 263 undefined on input line 600.

[263]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C1759D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 264 undefined on input
 line 647.

[264]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

LaTeX Warning: Citation `yeung2001' on page 265 undefined on input line 660.


LaTeX Warning: Citation `golub1971' on page 265 undefined on input line 668.


(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEA9D788471CB66B7D26E11C71E228
489B2.pygtex) [265]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABAB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961C9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750
 [] 
[266] [267]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F79D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 268 undefined on input
 line 802.


LaTeX Warning: Reference `sec:distancematrix' on page 268 undefined on input li
ne 805.


(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAF9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:clustercentroids' on page 268 undefined on input 
line 823.


(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FC9D788471CB66B7D26E11C71E228
489B2.pygtex) [268]

LaTeX Warning: Reference `sec:distancefunctions' on page 269 undefined on input
 line 846.


(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241D9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 269 undefined on input
 line 871.


(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E09D788471CB66B7D26E11C71E228
489B2.pygtex [269])

LaTeX Warning: Reference `sec:distancefunctions' on page 270 undefined on input
 line 900.


(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA85049D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:distancefunctions' on page 270 undefined on input
 line 922.

[270]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C49D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Citation `hihara2001' on page 271 undefined on input line 954.


(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D709D788471CB66B7D26E11C71E228
489B2.pygtex [271])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF589D788471CB66B7D26E11C71E228
489B2.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116
[]\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result
_K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT
1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 
. 
[272] (./Tutorial/chapter_learning.tex
Chapter 16.
[273]

LaTeX Warning: Reference `eq:OP' on page 274 undefined on input line 40.


LaTeX Warning: Reference `eq:NOP' on page 274 undefined on input line 40.


LaTeX Warning: Reference `table:training' on page 274 undefined on input line 7
5.


(./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4D9D788471CB66B7D26E11C71E228
489B2.pygtex [274])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4F9D788471CB66B7D26E11C71E228
489B2.pygtex [275])
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB0969D788471CB66B7D26E11C71E228
489B2.pygtex [276])

LaTeX Warning: Reference `eq:OP' on page 277 undefined on input line 197.


LaTeX Warning: Reference `eq:NOP' on page 277 undefined on input line 197.


(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D4029D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A0129D788471CB66B7D26E11C71E228
489B2.pygtex [277])

LaTeX Warning: Reference `eq:OP' on page 278 undefined on input line 261.


LaTeX Warning: Reference `eq:NOP' on page 278 undefined on input line 261.


LaTeX Warning: Reference `eq:OP' on page 278 undefined on input line 263.


LaTeX Warning: Reference `eq:NOP' on page 278 undefined on input line 263.


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


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


LaTeX Warning: Reference `sec:LogisticRegression' on page 278 undefined on inpu
t line 273.


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


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


LaTeX Warning: Reference `table:training' on page 278 undefined on input line 2
77.


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E69D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:LogisticRegressionTraining' on page 278 undefined
 on input line 285.

[278]

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


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


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA5959D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B38BF6A3D910590D450B331A075B723C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC19D788471CB66B7D26E11C71E228
489B2.pygtex [279])
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A586FFDD9483C890754DBE5DFC4207109D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D359D788471CB66B7D26E11C71E228
489B2.pygtex [280])) [281] (./Tutorial/chapter_graphics.tex
Chapter 17.

LaTeX Warning: Citation `pritchard2006' on page 282 undefined on input line 18.



LaTeX Warning: Citation `toth2006' on page 282 undefined on input line 28.


LaTeX Warning: Citation `vanderauwera2009' on page 282 undefined on input line 
31.


LaTeX Warning: Reference `chapter:seq_annot' on page 282 undefined on input lin
e 36.


LaTeX Warning: Reference `chapter:seqio' on page 282 undefined on input line 36
.

[282]

LaTeX Warning: Reference `chapter:seqio' on page 283 undefined on input line 64
.


(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A0D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D816D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B035D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_linear' on page 283 undefined on input li
ne 136.


(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [283]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_circular' on page 284 undefined on input 
line 167.


(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [284 <./images/plasmid_linear.png (PNG copy)>])

LaTeX Warning: Reference `sec:seq_features' on page 285 undefined on input line
 220.

[285 <./images/plasmid_circular.png (PNG copy)>]
(./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF27D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A735D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_labels' on page 286 undefined on input l
ine 260.


(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D850D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [286]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_labels' on page 287 undefined on input l
ine 330.


LaTeX Warning: Reference `sec:gd_features_without_seqfeatures' on page 287 unde
fined on input line 339.


LaTeX Warning: Reference `sec:gd_feature_captions' on page 287 undefined on inp
ut line 339.


LaTeX Warning: Reference `sec:gd_features_without_seqfeatures' on page 287 unde
fined on input line 339.


LaTeX Warning: Reference `sec:gd_feature_captions' on page 287 undefined on inp
ut line 339.


LaTeX Warning: Reference `sec:gd_nice_example' on page 287 undefined on input l
ine 345.


(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B94D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [287] [288 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigils' on page 289 undefined on input line 38
7.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `sec:gd_sigils' on page 289 undefined on input line 40
3.


(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_arrow_shafts' on page 289 undefined on i
nput line 434.


LaTeX Warning: Reference `sec:gd_arrow_sigils' on page 289 undefined on input l
ine 439.


(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:gd_sigil_arrow_heads' on page 289 undefined on in
put line 463.


LaTeX Warning: Reference `sec:gd_arrow_sigils' on page 289 undefined on input l
ine 468.


(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `sec:gd_top_down' on page 289 undefined on input line 
488.


(./_minted-Tutorial/67B3F646AA5F8690151428081229D39BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [289] [290 <./images/GD_sigils.png>] [291 <./images/GD_sigil_arrow
_shafts.png>] [292 <./images/GD_sigil_arrow_heads.png>] [293])
Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:plasmid_linear_nice' on page 294 undefined on inp
ut line 570.


LaTeX Warning: Reference `fig:plasmid_circular_nice' on page 294 undefined on i
nput line 571.


LaTeX Warning: Reference `sec:gd_nice_example' on page 294 undefined on input l
ine 577.


LaTeX Warning: Reference `sec:gd_nice_example' on page 294 undefined on input l
ine 577.


LaTeX Warning: Reference `sec:gd_nice_example' on page 294 undefined on input l
ine 585.


LaTeX Warning: Reference `sec:gd_nice_example' on page 294 undefined on input l
ine 585.


LaTeX Warning: Citation `proux2002' on page 294 undefined on input line 596.


LaTeX Warning: Reference `sec:efetch' on page 294 undefined on input line 605.


LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 294 undefined on input
 line 608.


LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 294 undefin
ed on input line 610.

[294 <./images/plasmid_linear_nice.png (PNG copy)>] [295 <./images/plasmid_circ
ular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA89D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [296])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [297]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:three_track_simple' on page 298 undefined on inpu
t line 732.


LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 298 undefined on inpu
t line 739.


LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 298 undefined on inpu
t line 739.


LaTeX Warning: Citation `proux2002' on page 298 undefined on input line 759.


(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA111D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [298 <./images/three_track_simple.png>])
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD1840D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [299])
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C28D5CCE6351B83FE352E9906AED2A
3B7C6.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 300 undefined on input li
ne 894.


LaTeX Warning: Reference `sec:gd_cross_links' on page 300 undefined on input li
ne 901.


LaTeX Warning: Reference `sec:gd_cross_links' on page 300 undefined on input li
ne 901.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:three_track_cl2' on page 300 undefined on input l
ine 927.


LaTeX Warning: Reference `sec:gd_cross_links' on page 300 undefined on input li
ne 934.


LaTeX Warning: Reference `sec:gd_cross_links' on page 300 undefined on input li
ne 934.

[300] [301 <./images/three_track_cl.png>] [302 <./images/three_track_cl2a.png>]

(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F728414977D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAFD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Citation `jupe2012' on page 303 undefined on input line 1012.


(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [303] [304 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])

(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [305]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:simplechromosome' on page 306 undefined on input 
line 1114.


(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A75D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [306]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:simplechromosome' on page 307 undefined on input 
line 1194.

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

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C719D788471CB66B7D26E11C71E228
489B2.pygtex) [308]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [309])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)) [310] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8D9D788471CB66B7D26E11C71E228
489B2.pygtex) [311]
(./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA97219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB449D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB0819D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF89D788471CB66B7D26E11C71E228
489B2.pygtex [312])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D72069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579D9D788471CB66B7D26E11C71E228
489B2.pygtex [313])
(./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E08721889D788471CB66B7D26E11C71E228
489B2.pygtex [314])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E69D788471CB66B7D26E11C71E228
489B2.pygtex)) [315] (./Tutorial/chapter_cookbook.tex
Chapter 20.

LaTeX Warning: Reference `chapter:seqio' on page 316 undefined on input line 22
.


(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [316])

LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 317 undefined on i
nput line 58.


(./_minted-Tutorial/CA0835D76EF6887731674D8AB555091BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E571649D788471CB66B7D26E11C71E228
489B2.pygtex) [317]
(./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD49D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 318 undefined on 
input line 146.


(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [318])

LaTeX Warning: Reference `sec:translation' on page 319 undefined on input line 
201.


LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 319 undefined o
n input line 206.


(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F64D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A0239647061D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [319])
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC65541D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE408793D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `sec:seqio-index-getraw' on page 320 undefined on inpu
t line 338.

[320]
(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [321]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF641831D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F35450D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 322 undefined on i
nput line 443.


LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 322 undefined on i
nput line 457.


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

(./_minted-Tutorial/AB16E58608A2F17CC79E692955720887D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [322])
Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477
\OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849.
fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[
]primer.fastq\OT1/cmr/m/n/10 . 

LaTeX Warning: Reference `sec:SeqRecord-slicing' on page 323 undefined on input
 line 480.


(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA556D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [323])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [324]
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F8915D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `sec:SeqIO-conversion' on page 325 undefined on input 
line 643.


LaTeX Warning: Citation `cock2010' on page 325 undefined on input line 646.

[325]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C31D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC40737367D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D25879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B6D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [326])
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CABD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A0D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `sec:SeqIO-index' on page 327 undefined on input line 
801.


(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582E9D788471CB66B7D26E11C71E228
489B2.pygtex [327])

LaTeX Warning: Reference `sec:SeqIO-index' on page 328 undefined on input line 
823.


LaTeX Warning: Reference `sec:SeqIO-sort' on page 328 undefined on input line 8
25.


LaTeX Warning: Reference `sec:SeqIO-conversion' on page 328 undefined on input 
line 839.


(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7D9D788471CB66B7D26E11C71E228
489B2.pygtex [328])

LaTeX Warning: Reference `sec:translation' on page 329 undefined on input line 
905.


(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF0989D788471CB66B7D26E11C71E228
489B2.pygtex) [329]
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [330])

LaTeX Warning: Reference `sec:gd_nice_example' on page 331 undefined on input l
ine 1024.


LaTeX Warning: Reference `chapter:seqio' on page 331 undefined on input line 10
41.


(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [331]) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:seq-len-hist' on page 332 undefined on input line
 1109.


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

(./_minted-Tutorial/798776F436EA559BACD9C305C0997391D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [332 <./images/hist_plot.png>])
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:seq-gc-plot' on page 333 undefined on input line 
1177.


LaTeX Warning: Reference `fig:nuc-dot-plot' on page 333 undefined on input line
 1191.

Excluding 'htmlonly' comment. [333 <./images/gc_plot.png>]
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/80A47C8780CE3021D53829563E816656D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [334 <./images/dot_plot.png>])
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F4D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:nuc-dot-plot' on page 335 undefined on input line
 1269.


(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B3D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/6655B5CD97C33186A22E6897501301FFD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [335])
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20ADD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.

LaTeX Warning: Reference `fig:nuc-dot-plot-scatter' on page 336 undefined on in
put line 1345.

[336 <./images/dot_plot_scatter.png>]
(./_minted-Tutorial/601CCA4B782F1DA528DB81B024803195D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `fig:paired-end-qual-plot' on page 337 undefined on in
put line 1406.

Excluding 'htmlonly' comment.

LaTeX Warning: Reference `chapter:align' on page 337 undefined on input line 14
18.


LaTeX Warning: Reference `chapter:align' on page 337 undefined on input line 14
25.


(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC73D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `sec:consensus' on page 337 undefined on input line 14
36.


LaTeX Warning: Reference `sec:pssm' on page 337 undefined on input line 1437.

[337]

LaTeX Warning: Reference `sec:getting_info_content' on page 338 undefined on in
put line 1438.


LaTeX Warning: Reference `sec:sub_matrix' on page 338 undefined on input line 1
439.


LaTeX Warning: Reference `sec:summary_info' on page 338 undefined on input line
 1445.


(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA3D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [338 <./images/SRR001666.png>]
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA4814535D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529
[]\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l
ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c
mr/m/n/10 .

(./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFF9D788471CB66B7D26E11C71E228
489B2.pygtex [339])

LaTeX Warning: Reference `sec:summary_info' on page 340 undefined on input line
 1565.


(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB530065D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A40D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D043D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [340])
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C9739D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `sec:align_clustal' on page 341 undefined on input lin
e 1640.


(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FA9D788471CB66B7D26E11C71E228
489B2.pygtex [341])
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C07179D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C379D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B494079159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704
\OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 
val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec
ted_frequencies[^^MD^^M, ^^ME^^M]

(./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF749D788471CB66B7D26E11C71E228
489B2.pygtex [342])
(./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4F9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Reference `chapter:seqio' on page 343 undefined on input line 17
48.

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

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD062141CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0441CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907341CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)

LaTeX Warning: Reference `sec:doctest' on page 344 undefined on input line 55.


(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D41CFBAB8D39E8FFAF3C5D885168
6F649.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
[344]
(./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex [345])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [346]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [347])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F441CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)

LaTeX Warning: Reference `sec:doctest' on page 348 undefined on input line 282.



(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA29D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B8297711D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [348])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex) [349]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345641CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4341CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)) [350] (./Tutorial/chapter_contributing.tex
Chapter 22.

LaTeX Warning: Reference `chapter:cookbook' on page 351 undefined on input line
 32.

[351]
(./_minted-Tutorial/7713FA97EA16E9508BA3E6B94494492541CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3641CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)

LaTeX Warning: Reference `chapter:testing' on page 352 undefined on input line 
85.


LaTeX Warning: Reference `chapter:testing' on page 352 undefined on input line 
101.

[352]) [353] (./Tutorial/chapter_appendix.tex
Chapter 23.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D329D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A462859D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B42D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [354])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C42D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)

LaTeX Warning: Reference `sec:SeqIO_compressed' on page 355 undefined on input 
line 91.


(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A2039D788471CB66B7D26E11C71E228
489B2.pygtex)) [355] [356] [357] [358] (./Tutorial.aux
(./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux)
(./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux)
(./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux)
(./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux)
(./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux)
(./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux)
(./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux)
(./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux)
(./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux)
(./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux)
(./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux)
(./Tutorial/chapter_appendix.aux))
kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000
mkdir: cannot create directory '././sbuild-nonexistent': Permission denied
mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000
This is METAFONT, Version 2.71828182 (TeX Live 2022/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 (359 pages, 2458924 bytes).
Transcript written on Tutorial.log.
pdflatex --shell-escape "\def\bpversion{1.80}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2022-11-01>
L3 programming layer <2022-11-02> (./Tutorial.tex
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2022/07/02 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty)
(/usr/share/texmf/tex/latex/misc/hevea.sty
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') Excluding comment 'rawhtml'
Excluding comment 'htmlonly')
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/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/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

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

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

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

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

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


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

(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/C3217FD04973F24516F5530BB525A22C9D788471CB66B7D26E11C71E228
489B2.pygtex) [11 <./images/biopython_logo_old.jpg>]
Overfull \hbox (2.99303pt too wide) in paragraph at lines 187--189
\OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor
t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or
 see [][]$\OT1/cmtt/m/n/10 http : / / biopython .
[12]) [13] (./Tutorial/chapter_quick_start.tex
Chapter 2.

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


(./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612C9D788471CB66B7D26E11C71E228
489B2.pygtex [14])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535AB9D788471CB66B7D26E11C71E228
489B2.pygtex) [15]
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B02133467818559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26D9D788471CB66B7D26E11C71E228
489B2.pygtex [16])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F29D788471CB66B7D26E11C71E228
489B2.pygtex) [17]) [18] (./Tutorial/chapter_seq_objects.tex
Chapter 3.

(./_minted-Tutorial/048D805D0CE39D0271B0A9A9F6FA0B909D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDC9D788471CB66B7D26E11C71E228
489B2.pygtex) [19]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0F44B540F3531194878FC29AF0179029D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E976225049D788471CB66B7D26E11C71E228
489B2.pygtex [20])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D93864209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/732D927996C79742AC990312B3D6EEB09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C2709D788471CB66B7D26E11C71E228
489B2.pygtex [21])
(./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC479D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D3949D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8D9D788471CB66B7D26E11C71E228
489B2.pygtex [22])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF179D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC09D788471CB66B7D26E11C71E228
489B2.pygtex [23])
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C87539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B3869D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A709D788471CB66B7D26E11C71E228
489B2.pygtex [24])
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD649D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF989D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE799D788471CB66B7D26E11C71E228
489B2.pygtex [25])
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B559909D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874D9D788471CB66B7D26E11C71E228
489B2.pygtex [26])
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/06DBC59F2EAD33E7A9518885378766159D788471CB66B7D26E11C71E228
489B2.pygtex) [27]
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C3389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CBEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [28])
(./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E849D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DFDB859800920408E228736AD921B5DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B0409D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE4519D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2E9D788471CB66B7D26E11C71E228
489B2.pygtex [29])
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C09D788471CB66B7D26E11C71E228
489B2.pygtex)) [30] [31] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

(./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC8099D788471CB66B7D26E11C71E228
489B2.pygtex) [32]
(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D4079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC29D788471CB66B7D26E11C71E228
489B2.pygtex [33])
(./_minted-Tutorial/510764EE0BB38AD6C688E71989677507EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D8498229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD20859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [34])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4AEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA6019D788471CB66B7D26E11C71E228
489B2.pygtex [35])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F9269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0D9D788471CB66B7D26E11C71E228
489B2.pygtex) [36] [37]
(./_minted-Tutorial/AD47AD29D6F7927F9406BE56096763889D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F39D788471CB66B7D26E11C71E228
489B2.pygtex [38])
(./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D86C559003980DC8749AF92530435DFD9D788471CB66B7D26E11C71E228
489B2.pygtex) [39]
(./_minted-Tutorial/1C0A562378DEEE8E210765437B3E17009D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B499D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0C3ED75879971F09D72A92585654A32C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E39209D788471CB66B7D26E11C71E228
489B2.pygtex [40])
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F96899D788471CB66B7D26E11C71E228
489B2.pygtex [41])
(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B23409D788471CB66B7D26E11C71E228
489B2.pygtex [42])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEB9D788471CB66B7D26E11C71E228
489B2.pygtex) [43]
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B3119D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D24579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDF9D788471CB66B7D26E11C71E228
489B2.pygtex [44])
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF17185016699D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3E9D788471CB66B7D26E11C71E228
489B2.pygtex [45])
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B639D788471CB66B7D26E11C71E228
489B2.pygtex [46])
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B87939D788471CB66B7D26E11C71E228
489B2.pygtex)) [47] (./Tutorial/chapter_seqio.tex
Chapter 5.

(./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D4989D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB678D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [48])
(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE500954D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F1D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [49])
(./_minted-Tutorial/C82398A4A04383A063D2E64881123052D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AEDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [50]
(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD162221D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD82D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE69D788471CB66B7D26E11C71E228
489B2.pygtex [51])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E73451D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9562C263804C6DD613F075A435553A9F9D788471CB66B7D26E11C71E228
489B2.pygtex [52])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C919D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/23394A4616015FFE4619934E984241789D788471CB66B7D26E11C71E228
489B2.pygtex [53])
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C099D788471CB66B7D26E11C71E228
489B2.pygtex) [54]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD476D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD8D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [55])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A4D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989F9D788471CB66B7D26E11C71E228
489B2.pygtex [56])
(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF69D788471CB66B7D26E11C71E228
489B2.pygtex [57])
(./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528FEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/55430EAFE498E385842834603E0B8C86D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB8D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [58])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C1788939D788471CB66B7D26E11C71E228
489B2.pygtex) [59]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF40659D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A3649D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D66D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE9D788471CB66B7D26E11C71E228
489B2.pygtex [60])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853
\OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org /
 pub / databases / uniprot / current _ release / knowledgebase / complete /

(./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929D9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894
[]\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u
p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1
/cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C141CFBAB8D39E8FFAF3C5D885168
6F649.pygtex [61])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41041CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A27779D788471CB66B7D26E11C71E228
489B2.pygtex) [62]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C64719D788471CB66B7D26E11C71E228
489B2.pygtex) [63]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD7342D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [64])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [65])
(./_minted-Tutorial/C194E2231D844AE7D0223173D2A89991D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEA9D788471CB66B7D26E11C71E228
489B2.pygtex) [66]
(./_minted-Tutorial/920133226A22EEB682D854077D7FB78F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C2600289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E381FF526AC999B71717F178C997F6B29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26A9D788471CB66B7D26E11C71E228
489B2.pygtex) [67]
(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EAD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F53D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351
\OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) 
[]\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm
tt/m/n/10 SeqRecord.format(...)
[68]
(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397
[]\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm
tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt
/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D749A84299CF58E876E9A899069830DBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)) [69] (./Tutorial/chapter_align.tex
Chapter 6.

(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [70])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AEC9D788471CB66B7D26E11C71E228
489B2.pygtex [71])
(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A310779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [72]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C5604079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [73])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF7569D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DEEF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [74]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [75])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [76]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D3189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [77])
Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435
\OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t
or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()

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

(./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F40249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479FEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [78])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [79])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F16D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [80])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2590B11C695B984E246A0A91734F786C9D788471CB66B7D26E11C71E228
489B2.pygtex) [81]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE59D788471CB66B7D26E11C71E228
489B2.pygtex [82])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B716929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB009D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E599D788471CB66B7D26E11C71E228
489B2.pygtex [83])
(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A92539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AE857C14E4731CC6F6EBA530514600979D788471CB66B7D26E11C71E228
489B2.pygtex) [84]
(./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/523928538FA511A925EC995B1803BD169D788471CB66B7D26E11C71E228
489B2.pygtex) [85]
(./_minted-Tutorial/CD47D1913C82182C164BD47DA47152829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E8939D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C630649D788471CB66B7D26E11C71E228
489B2.pygtex) [86]
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A4429D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F9863689D788471CB66B7D26E11C71E228
489B2.pygtex [87])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B0459D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B274259D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130
[]\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi
le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO

(./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BD9D788471CB66B7D26E11C71E228
489B2.pygtex [88])
(./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F7399989D788471CB66B7D26E11C71E228
489B2.pygtex [89])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E74549D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C9D788471CB66B7D26E11C71E228
489B2.pygtex [90])
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE749D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A2409D788471CB66B7D26E11C71E228
489B2.pygtex) [91]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/39152F199CEBB3375366F2E9478245199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF3856749D788471CB66B7D26E11C71E228
489B2.pygtex [92])
(./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE24939D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DF151703751D72BD556402B910190A879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA889D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/554024580088332FAF0EA9296BACE82E9D788471CB66B7D26E11C71E228
489B2.pygtex) [93]
(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E3619D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6CCC707502EDD92E9C355854215BF8859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C59D788471CB66B7D26E11C71E228
489B2.pygtex [94])
(./_minted-Tutorial/E5E00F47BD7A0C8BC5F88185262838689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE049D788471CB66B7D26E11C71E228
489B2.pygtex) [95]
(./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/48453D528762FF183499778647AF218B9D788471CB66B7D26E11C71E228
489B2.pygtex [96])
(./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A399D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix
 []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu
tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt
t/m/n/10 aligner.mismatch_score

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

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


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

(./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CE9D788471CB66B7D26E11C71E228
489B2.pygtex [97]) [98] [99]
(./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514A9D788471CB66B7D26E11C71E228
489B2.pygtex) [100]
(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE19119D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB86719D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EF9D788471CB66B7D26E11C71E228
489B2.pygtex [101])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D019D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9F9D788471CB66B7D26E11C71E228
489B2.pygtex [102])
(./_minted-Tutorial/0758643069FF669538B9540ECD26C94C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A342965929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/76E331C5187C259B69198E91FC4AD1129D788471CB66B7D26E11C71E228
489B2.pygtex [103])
(./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD3579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966B9D788471CB66B7D26E11C71E228
489B2.pygtex [104])
(./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/66AABFA387595237A8CE2518915213F89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B15E737F9393063B641148640673D9919D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B469D788471CB66B7D26E11C71E228
489B2.pygtex [105])
(./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/874975627BAB24A36A35FD4C633D246D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BD9D788471CB66B7D26E11C71E228
489B2.pygtex [106])
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A79D788471CB66B7D26E11C71E228
489B2.pygtex [107])
(./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/52868B2F44504455E4969FEF2614B63B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB949D788471CB66B7D26E11C71E228
489B2.pygtex) [108]
(./_minted-Tutorial/E7E68A8851DEEE300947A0531513417D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF659D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA17339D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6502BA65433924876427DBB6013C10039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FD9D788471CB66B7D26E11C71E228
489B2.pygtex [109])
(./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F10129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA50779D788471CB66B7D26E11C71E228
489B2.pygtex [110])
(./_minted-Tutorial/779C61444C54C1736794F4E11B0E326D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E1059D788471CB66B7D26E11C71E228
489B2.pygtex [111])
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF7966009D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613
\OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments 
is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing
 [][]\OT1/cmtt/m/n/10 len(alignments)

(./_minted-Tutorial/F89522EF58FB067C6521C367C71347169D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9C9D788471CB66B7D26E11C71E228
489B2.pygtex [112])
(./_minted-Tutorial/882BD2544386DECA236BF25C7DD648579D788471CB66B7D26E11C71E228
489B2.pygtex [113])
(./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA709D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A299D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/13D646E6B49807044DBDC43707A098469D788471CB66B7D26E11C71E228
489B2.pygtex [114])
(./_minted-Tutorial/467CA50C36874E405E988587FEC076869D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E629D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A94C18D2207C354646F831D57FD85B359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D89D788471CB66B7D26E11C71E228
489B2.pygtex [115])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A739D788471CB66B7D26E11C71E228
489B2.pygtex [116])
(./_minted-Tutorial/AAF53200644F4F68779FB844730087D39D788471CB66B7D26E11C71E228
489B2.pygtex [117])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057D9D788471CB66B7D26E11C71E228
489B2.pygtex [118])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BAB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/842D73F66680850822D006857AE71FE79D788471CB66B7D26E11C71E228
489B2.pygtex) [119]
(./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE31359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7C466424D72F09AE5AACA884161416F99D788471CB66B7D26E11C71E228
489B2.pygtex [120])
(./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA8252789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F6800939D788471CB66B7D26E11C71E228
489B2.pygtex [121])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315EC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D862416647079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [122])
(./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/60D893638743BD147116D13E00593D6C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [123])
(./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9ED9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6D9D788471CB66B7D26E11C71E228
489B2.pygtex [124])
(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F25199D788471CB66B7D26E11C71E228
489B2.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED09D788471CB66B7D26E11C71E228
489B2.pygtex) [125]
(./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F120EF3444F3192D48657B4E524070179D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F20919D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5D9D788471CB66B7D26E11C71E228
489B2.pygtex [126])
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C719D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A9D788471CB66B7D26E11C71E228
489B2.pygtex [127])) [128] (./Tutorial/chapter_blast.tex
Chapter 7.

Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46
[]\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas
t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs 
&
[129]
(./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4E9D788471CB66B7D26E11C71E228
489B2.pygtex [130])
(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C2049D788471CB66B7D26E11C71E228
489B2.pygtex) [131]
(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE47929D788471CB66B7D26E11C71E228
489B2.pygtex) [132]
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C2049D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE52180049D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F403949D788471CB66B7D26E11C71E228
489B2.pygtex [133])
(./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D2389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68259DF5B1930070C029D5A72D891A369D788471CB66B7D26E11C71E228
489B2.pygtex [134])
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.

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

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

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [138]
Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93
[][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle 
con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10
 HSPFragment

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

(./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FC9D788471CB66B7D26E11C71E228
489B2.pygtex [139])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B519559D788471CB66B7D26E11C71E228
489B2.pygtex [140])
(./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/362861C831165FEA5413E0240053CD899D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE3279D788471CB66B7D26E11C71E228
489B2.pygtex [141])
(./_minted-Tutorial/FD9C81C098491598DBFB6208173BB5759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A039D788471CB66B7D26E11C71E228
489B2.pygtex) [142]
(./_minted-Tutorial/0B914838010D3E86EC368E1702EB72539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E6199D788471CB66B7D26E11C71E228
489B2.pygtex [143])
(./_minted-Tutorial/DDECA9EB99D9FA38003A52C1765930729D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/578CBF904F35965EECFEC1FA694F07529D788471CB66B7D26E11C71E228
489B2.pygtex [144])
(./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD649D788471CB66B7D26E11C71E228
489B2.pygtex) [145]
(./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC62468639D788471CB66B7D26E11C71E228
489B2.pygtex) [146]
(./_minted-Tutorial/A3385B945E43CC076FFA693B27681F059D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE5735779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B469D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD959D788471CB66B7D26E11C71E228
489B2.pygtex [147])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD8804449D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C7879D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745
[]\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10
 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr
/m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment

(./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A35369099D788471CB66B7D26E11C71E228
489B2.pygtex [148])
(./_minted-Tutorial/16771935702D6A2A9762A80A621013D89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/046FE550C51B323D1E952A27E126FE199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A55E467518B2E0F936A232F0970B10379D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB20219D788471CB66B7D26E11C71E228
489B2.pygtex [149])
(./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EED9D788471CB66B7D26E11C71E228
489B2.pygtex [150])
(./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D339D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/758BAC7574A59544686354199D20892C9D788471CB66B7D26E11C71E228
489B2.pygtex) [151]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA99D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059
\OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT
1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like 
[][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F49D788471CB66B7D26E11C71E228
489B2.pygtex) [152]
Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092
[]\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us
-ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt
/m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E98689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DE9D788471CB66B7D26E11C71E228
489B2.pygtex) [153]
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170
[]\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 
also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic
h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse

(./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C1769D788471CB66B7D26E11C71E228
489B2.pygtex)) [154] (./Tutorial/chapter_entrez.tex
Chapter 9.
[155]
(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB59D788471CB66B7D26E11C71E228
489B2.pygtex) [156]
(./_minted-Tutorial/7692669934D8ED6DEE1B8B66847454219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA369D788471CB66B7D26E11C71E228
489B2.pygtex [157])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C0089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FAC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F69D788471CB66B7D26E11C71E228
489B2.pygtex [158])
(./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D502779D788471CB66B7D26E11C71E228
489B2.pygtex) [159]
(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19F9D788471CB66B7D26E11C71E228
489B2.pygtex) [160]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F31479D788471CB66B7D26E11C71E228
489B2.pygtex [161] [162])
(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [163])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F4879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF0089D788471CB66B7D26E11C71E228
489B2.pygtex [164])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68622353B578A611D2F621023E3C4BD19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F709D788471CB66B7D26E11C71E228
489B2.pygtex [165])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0941CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722A9D788471CB66B7D26E11C71E228
489B2.pygtex [166])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF38EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [167]
(./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1BEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [168])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB99D788471CB66B7D26E11C71E228
489B2.pygtex) [169]
(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AADEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC39D788471CB66B7D26E11C71E228
489B2.pygtex [170])
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E2779D788471CB66B7D26E11C71E228
489B2.pygtex) [171]
(./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A12669D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [172])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B6249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE19D788471CB66B7D26E11C71E228
489B2.pygtex) [173]
(./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA1D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71A9D788471CB66B7D26E11C71E228
489B2.pygtex [174])
(./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD09D788471CB66B7D26E11C71E228
489B2.pygtex) [175]
(./_minted-Tutorial/964257041BEB9E732FF9A943209BD6ED9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/600193D5D5D44162E61A3CAB404484269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B6420389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C59D788471CB66B7D26E11C71E228
489B2.pygtex [176])
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2F9D788471CB66B7D26E11C71E228
489B2.pygtex [177])
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A727979D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB38489D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D76169664531538D144C55FFC33571B9D788471CB66B7D26E11C71E228
489B2.pygtex [178])
(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C459D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB936499D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D89D788471CB66B7D26E11C71E228
489B2.pygtex) [179]
(./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C4779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F96339D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D574D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [180])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFAD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [181])
(./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927A9D788471CB66B7D26E11C71E228
489B2.pygtex)) [182] (./Tutorial/chapter_uniprot.tex
Chapter 10.

(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A869D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A6689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD67689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/930B60BD569CAAF368B0E614553F30309D788471CB66B7D26E11C71E228
489B2.pygtex) [183]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA65191829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB9346699D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD692289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D149D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C069D788471CB66B7D26E11C71E228
489B2.pygtex [184])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A45179189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09AB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [185])
(./_minted-Tutorial/956383F4066B9E093C9D2E3843CA02209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307B9D788471CB66B7D26E11C71E228
489B2.pygtex [186])
(./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E29D788471CB66B7D26E11C71E228
489B2.pygtex) [187]
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5BEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC7839D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF99D788471CB66B7D26E11C71E228
489B2.pygtex [188])
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B6229D788471CB66B7D26E11C71E228
489B2.pygtex [189])
Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366
[]\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n
/10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/
m/n/10 SwissProt.read(handle)

(./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87D9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410
[]\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m
en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re
cord

(./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B7539D788471CB66B7D26E11C71E228
489B2.pygtex) [190]
(./_minted-Tutorial/9457A436D281E066D350873A88476E599D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E79D788471CB66B7D26E11C71E228
489B2.pygtex [191])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E861699D788471CB66B7D26E11C71E228
489B2.pygtex)) [192] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C228539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E690859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C719D788471CB66B7D26E11C71E228
489B2.pygtex [193])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA73889D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB82319D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879E9D788471CB66B7D26E11C71E228
489B2.pygtex) [194]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D1769D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A0249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A59D788471CB66B7D26E11C71E228
489B2.pygtex) [195]
(./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB1369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECEC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA49D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264
\OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m
/n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato
m)
[196] Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D9799D788471CB66B7D26E11C71E228
489B2.pygtex) [197] [198 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD8559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB2479D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E27276229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A129D788471CB66B7D26E11C71E228
489B2.pygtex) [199]
(./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DC9D788471CB66B7D26E11C71E228
489B2.pygtex) [200]
(./_minted-Tutorial/35E34E333445AAAA4E33570211335BA59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B19D788471CB66B7D26E11C71E228
489B2.pygtex [201])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC880989D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB124929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/76657140082404C594EE786B642215C39D788471CB66B7D26E11C71E228
489B2.pygtex [202])
(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254C9D788471CB66B7D26E11C71E228
489B2.pygtex) [203]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB909D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B1289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B39D788471CB66B7D26E11C71E228
489B2.pygtex [204])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF2318999D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A6249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC26639D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA399D788471CB66B7D26E11C71E228
489B2.pygtex [205])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E6679D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899B9D788471CB66B7D26E11C71E228
489B2.pygtex [206])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B33389074760A02AC27316E67DAAB0739D788471CB66B7D26E11C71E228
489B2.pygtex [207])
Overfull \hbox (42.26714pt too wide) in paragraph at lines 956--960
\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 976--996
[][] 
[208]
(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993C9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Command \r invalid in math mode on input line 1049.


(./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705E9D788471CB66B7D26E11C71E228
489B2.pygtex) [209]
(./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C67099D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/895E3343902EFB0E5475667B01C4B6919D788471CB66B7D26E11C71E228
489B2.pygtex) [210] [211]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A749D788471CB66B7D26E11C71E228
489B2.pygtex [212])
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5D9D788471CB66B7D26E11C71E228
489B2.pygtex) [213]) [214] (./Tutorial/chapter_popgen.tex
Chapter 12.

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [215]
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)) [216] (./Tutorial/chapter_phylo.tex
Chapter 13.

(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15841CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4AD9D788471CB66B7D26E11C71E228
489B2.pygtex [217])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B99D788471CB66B7D26E11C71E228
489B2.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA9D788471CB66B7D26E11C71E228
489B2.pygtex) [218]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185
[]\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t
he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor

(./_minted-Tutorial/29624A9666C9430AABADF395148BBF279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B99D788471CB66B7D26E11C71E228
489B2.pygtex [219 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9B9D788471CB66B7D26E11C71E228
489B2.pygtex [220 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/456F5679DCD4FF740E7A110889D865739D788471CB66B7D26E11C71E228
489B2.pygtex [221])
(./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D39D788471CB66B7D26E11C71E228
489B2.pygtex [222])
(./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEE9D788471CB66B7D26E11C71E228
489B2.pygtex) Excluding 'htmlonly' comment. [223 <./images/phylo-draw-example.p
ng>]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486
\OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, 
[][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"})
[224]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537
[]\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, 
find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10
 ,
[225]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF6D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [226]
Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707
[]\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter
-act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier .

(./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD81199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095B9D788471CB66B7D26E11C71E228
489B2.pygtex) [227]
(./_minted-Tutorial/0702C9875263768417DD3ED2EF78755E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D29D788471CB66B7D26E11C71E228
489B2.pygtex) [228]) [229] (./Tutorial/chapter_motifs.tex
Chapter 14.

(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486A9D788471CB66B7D26E11C71E228
489B2.pygtex [230])
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D1779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D2571739D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/86717C2BCE65F41FCDB86527631658579D788471CB66B7D26E11C71E228
489B2.pygtex [231])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F612431920229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB24769D788471CB66B7D26E11C71E228
489B2.pygtex) [232]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [233])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECD9D788471CB66B7D26E11C71E228
489B2.pygtex [234])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C769D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [235])
(./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F7069D788471CB66B7D26E11C71E228
489B2.pygtex [236])
(./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DC9D788471CB66B7D26E11C71E228
489B2.pygtex [237])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFD9D788471CB66B7D26E11C71E228
489B2.pygtex [238])
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C3789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6B9D788471CB66B7D26E11C71E228
489B2.pygtex [239])
(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6ABEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [240])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909F9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606
\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man
d reads the com-plete file di-rectly, so you can close the file af-ter call-ing
 [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B849D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB69D788471CB66B7D26E11C71E228
489B2.pygtex [241])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E0120539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [242])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5C9D788471CB66B7D26E11C71E228
489B2.pygtex)

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

[243]
(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EF9D788471CB66B7D26E11C71E228
489B2.pygtex [244])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F264069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF514959D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE706059D788471CB66B7D26E11C71E228
489B2.pygtex [245])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C749D788471CB66B7D26E11C71E228
489B2.pygtex [246])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C988129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E2259D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E489D788471CB66B7D26E11C71E228
489B2.pygtex [247])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7B9D788471CB66B7D26E11C71E228
489B2.pygtex [248])
(./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A819D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA1619D788471CB66B7D26E11C71E228
489B2.pygtex) [249]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E259D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A50929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C860739D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE9709D788471CB66B7D26E11C71E228
489B2.pygtex [250])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF49D788471CB66B7D26E11C71E228
489B2.pygtex [251])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E3229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD72616039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA24739D788471CB66B7D26E11C71E228
489B2.pygtex [252])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA169D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D39D788471CB66B7D26E11C71E228
489B2.pygtex) [253]
(./_minted-Tutorial/868ABF9ABD2736A12F423306646D77069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/912C817861E626118AB2FA06F12910B69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [254]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB419D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B69D788471CB66B7D26E11C71E228
489B2.pygtex) [255]) [256] (./Tutorial/chapter_cluster.tex
Chapter 15.
[257] [258] [259] [260]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED41409D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C2B72A7408C7DF74DFCEBE04859972879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE6017358279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A2500D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C09D788471CB66B7D26E11C71E228
489B2.pygtex [261])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246
\OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra
nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$

(./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB349D788471CB66B7D26E11C71E228
489B2.pygtex) [262] [263]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E9D788471CB66B7D26E11C71E228
489B2.pygtex) [264]
(./_minted-Tutorial/C286E2777B917B774560CBDC7CF926269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED18D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7ACD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [265] [266]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424
[][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them.
 The items be-ing clus-tered are num-bered from 0 to $[]$,

(./_minted-Tutorial/015798D317E9D8732518AFD186C997CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C2390492678617399D788471CB66B7D26E11C71E228
489B2.pygtex) [267]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE229D788471CB66B7D26E11C71E228
489B2.pygtex) [268]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F729D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D419D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF88950559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEB9D788471CB66B7D26E11C71E228
489B2.pygtex [269])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED18D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7ACD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [270]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C1759D788471CB66B7D26E11C71E228
489B2.pygtex) [271]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEA9D788471CB66B7D26E11C71E228
489B2.pygtex) [272]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABAB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961C9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750
 [] 
[273] [274]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FC9D788471CB66B7D26E11C71E228
489B2.pygtex) [275]
(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E09D788471CB66B7D26E11C71E228
489B2.pygtex [276])
(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA85049D788471CB66B7D26E11C71E228
489B2.pygtex) [277]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D709D788471CB66B7D26E11C71E228
489B2.pygtex [278])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF589D788471CB66B7D26E11C71E228
489B2.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116
[]\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result
_K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT
1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 
. 
[279] (./Tutorial/chapter_learning.tex
Chapter 16.
[280]
(./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4D9D788471CB66B7D26E11C71E228
489B2.pygtex [281])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4F9D788471CB66B7D26E11C71E228
489B2.pygtex [282])
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB0969D788471CB66B7D26E11C71E228
489B2.pygtex [283])
(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D4029D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A0129D788471CB66B7D26E11C71E228
489B2.pygtex [284])

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


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


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


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


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E69D788471CB66B7D26E11C71E228
489B2.pygtex) [285]

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


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


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA5959D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B38BF6A3D910590D450B331A075B723C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC19D788471CB66B7D26E11C71E228
489B2.pygtex [286])
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A586FFDD9483C890754DBE5DFC4207109D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D359D788471CB66B7D26E11C71E228
489B2.pygtex [287])) [288] (./Tutorial/chapter_graphics.tex
Chapter 17.
[289]
(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A0D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D816D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B035D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [290]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [291 <./images/plasmid_linear.png (PNG copy)>]) [292 <./images/pla
smid_circular.png (PNG copy)>]
(./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF27D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A735D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D850D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [293]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B94D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [294] [295 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/67B3F646AA5F8690151428081229D39BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [296] [297 <./images/GD_sigils.png>] [298 <./images/GD_sigil_arrow
_shafts.png>] [299 <./images/GD_sigil_arrow_heads.png>] [300])
Excluding 'htmlonly' comment. [301 <./images/plasmid_linear_nice.png (PNG copy)
>] [302 <./images/plasmid_circular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA89D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [303])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [304]) Excluding 'htmlonly' comment. [305 <./images/three_track_si
mple.png>]
(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA111D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [306])
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD1840D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C28D5CCE6351B83FE352E9906AED2A
3B7C6.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. [307] Excluding 'htmlonly' comment. [308 <./image
s/three_track_cl.png>] [309 <./images/three_track_cl2a.png>]
(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F728414977D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAFD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [310]
(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [311] [312 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A75D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [313]) Excluding 'htmlonly' comment.) [314]
(./Tutorial/chapter_kegg.tex
Chapter 18.

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C719D788471CB66B7D26E11C71E228
489B2.pygtex) [315]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [316])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)) [317] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8D9D788471CB66B7D26E11C71E228
489B2.pygtex) [318]
(./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA97219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB449D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB0819D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF89D788471CB66B7D26E11C71E228
489B2.pygtex [319])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D72069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579D9D788471CB66B7D26E11C71E228
489B2.pygtex [320])
(./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E08721889D788471CB66B7D26E11C71E228
489B2.pygtex [321])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E69D788471CB66B7D26E11C71E228
489B2.pygtex)) [322] (./Tutorial/chapter_cookbook.tex
Chapter 20.

(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [323])
(./_minted-Tutorial/CA0835D76EF6887731674D8AB555091BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E571649D788471CB66B7D26E11C71E228
489B2.pygtex) [324]
(./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [325])
(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F64D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A0239647061D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [326])
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC65541D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE408793D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [327]
(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [328]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF641831D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F35450D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
Overfull \hbox (5.83499pt too wide) in paragraph at lines 454--458
\OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul
d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/AB16E58608A2F17CC79E692955720887D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [329])
Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477
\OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849.
fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[
]primer.fastq\OT1/cmr/m/n/10 . 

(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA556D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [330])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [331]
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F8915D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [332]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C31D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC40737367D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D25879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B6D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [333])
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CABD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A0D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582E9D788471CB66B7D26E11C71E228
489B2.pygtex [334])
(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7D9D788471CB66B7D26E11C71E228
489B2.pygtex [335])
(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF0989D788471CB66B7D26E11C71E228
489B2.pygtex) [336]
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [337])
(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [338]) Excluding 'htmlonly' comment.
Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120
[]\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10
 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use
 [][]\OT1/cmtt/m/n/10 pylab.savefig(...)

(./_minted-Tutorial/798776F436EA559BACD9C305C0997391D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [339 <./images/hist_plot.png>])
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
[340 <./images/gc_plot.png>]
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/80A47C8780CE3021D53829563E816656D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [341 <./images/dot_plot.png>])
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F4D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B3D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/6655B5CD97C33186A22E6897501301FFD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [342])
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20ADD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment. [343 <./images/dot_plot_scatter.png
>]
(./_minted-Tutorial/601CCA4B782F1DA528DB81B024803195D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC73D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [344]
(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA3D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [345 <./images/SRR001666.png>]
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA4814535D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529
[]\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l
ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c
mr/m/n/10 .

(./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFF9D788471CB66B7D26E11C71E228
489B2.pygtex [346])
(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB530065D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A40D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D043D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [347])
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C9739D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FA9D788471CB66B7D26E11C71E228
489B2.pygtex [348])
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C07179D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C379D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B494079159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704
\OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 
val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec
ted_frequencies[^^MD^^M, ^^ME^^M]

(./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF749D788471CB66B7D26E11C71E228
489B2.pygtex [349])
(./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4F9D788471CB66B7D26E11C71E228
489B2.pygtex)) [350] (./Tutorial/chapter_testing.tex
Chapter 21.

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD062141CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0441CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907341CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D41CFBAB8D39E8FFAF3C5D885168
6F649.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
[351]
(./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex [352])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [353]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [354])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F441CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA29D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B8297711D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [355])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex) [356]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345641CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4341CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)) [357] (./Tutorial/chapter_contributing.tex
Chapter 22.
[358]
(./_minted-Tutorial/7713FA97EA16E9508BA3E6B94494492541CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3641CFBAB8D39E8FFAF3C5D885168
6F649.pygtex) [359]) [360] (./Tutorial/chapter_appendix.tex
Chapter 23.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D329D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A462859D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B42D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [361])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C42D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A2039D788471CB66B7D26E11C71E228
489B2.pygtex)) [362] [363] [364] [365] (./Tutorial.aux
(./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux)
(./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux)
(./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux)
(./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux)
(./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux)
(./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux)
(./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux)
(./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux)
(./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux)
(./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux)
(./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux)
(./Tutorial/chapter_appendix.aux))

LaTeX Warning: There were undefined references.


LaTeX Warning: There were multiply-defined labels.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb
xti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmitt10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmr5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on Tutorial.pdf (366 pages, 2519602 bytes).
Transcript written on Tutorial.log.
pdflatex --shell-escape "\def\bpversion{1.80}\input{Tutorial}"
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2022-11-01>
L3 programming layer <2022-11-02> (./Tutorial.tex
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2022/07/02 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty)
(/usr/share/texmf/tex/latex/misc/hevea.sty
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') Excluding comment 'rawhtml'
Excluding comment 'htmlonly')
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/minted/minted.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/fvextra/fvextra.sty
(/usr/share/texlive/texmf-dist/tex/latex/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/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))

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

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

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

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

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


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

(./_minted-Tutorial/default.pygstyle)
(./_minted-Tutorial/C3217FD04973F24516F5530BB525A22C9D788471CB66B7D26E11C71E228
489B2.pygtex) [11 <./images/biopython_logo_old.jpg>]
Overfull \hbox (2.99303pt too wide) in paragraph at lines 187--189
\OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor
t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or
 see [][]$\OT1/cmtt/m/n/10 http : / / biopython .
[12]) [13] (./Tutorial/chapter_quick_start.tex
Chapter 2.

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


(./_minted-Tutorial/C083BA757ADC0A392BD8802D1351612C9D788471CB66B7D26E11C71E228
489B2.pygtex [14])
(./_minted-Tutorial/BCD1E3D53103B8919C8BBE66D33535AB9D788471CB66B7D26E11C71E228
489B2.pygtex) [15]
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/33F85FAC7266F854F2B02133467818559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57D5D2D450B93D59CC2D6708C6BA430B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9951EE2B2EB57108F1B91BF42B5EF26D9D788471CB66B7D26E11C71E228
489B2.pygtex [16])
(./_minted-Tutorial/D0C141F7F69A52FF8D2723831BF439F29D788471CB66B7D26E11C71E228
489B2.pygtex) [17]) [18] (./Tutorial/chapter_seq_objects.tex
Chapter 3.

(./_minted-Tutorial/048D805D0CE39D0271B0A9A9F6FA0B909D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CCFAD09A7C678CC6F23FB63113DD1EDC9D788471CB66B7D26E11C71E228
489B2.pygtex) [19]
(./_minted-Tutorial/FD65D36A7B14289ADEAB241851842BCA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0F44B540F3531194878FC29AF0179029D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/739024CAA2FC886FEC674E3B4C3FD3A49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EB307D8D2C6B186F102975D2F777C5C89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/504E820336D4D852A5104D8E976225049D788471CB66B7D26E11C71E228
489B2.pygtex [20])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6C027F180664948287C5ED0C06A70E369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8900FA9A050CA74204F5DCB8D93864209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5A43D1A8AC729BFB659D75BFD070C79A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/732D927996C79742AC990312B3D6EEB09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36BB9CB69ABA7149C7050E321F74C2709D788471CB66B7D26E11C71E228
489B2.pygtex [21])
(./_minted-Tutorial/14DC45CA9BEAFF3B8A49C8E43A9FF33C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4FC9049D1029A23D48B33F9D862ACC479D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E62329AC6ED4D8F7B1EF4988F8DBA19F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/008EC869056581873654FF9A8E92D3949D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/457BF67E0722BB5B93A17BD27C0B6D8D9D788471CB66B7D26E11C71E228
489B2.pygtex [22])
(./_minted-Tutorial/21058E2884DE0E2797798658CEC2E54F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/34FD0122B81370E5F3563284D60CFF179D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A54827F8BB70B416D99923FF5088CCC09D788471CB66B7D26E11C71E228
489B2.pygtex [23])
(./_minted-Tutorial/427B060556C1BB93F326E658CF6C87539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/692203B43955DEEBA597180E090EBEBD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0A4AF1735B84470B955325263082B3869D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F7FFCC027B254744B7B47314F48923FE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/186028EBD7A9B4B4276808BC5B218A709D788471CB66B7D26E11C71E228
489B2.pygtex [24])
(./_minted-Tutorial/2F42D08D321C7BC408E4704103B70F2E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/544C1E23D35FAC62FBE120AA24D6EF829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A487EC21D16913E80A948528AA61CD649D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7BC83BB268F7BA2D207FDE001034CF989D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/59D2BC7361BC3147180163BF1D4DDE799D788471CB66B7D26E11C71E228
489B2.pygtex [25])
(./_minted-Tutorial/087889BE640F25A1E1D26EB819B559909D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C387354CBEC6317F42CD9F596E775BE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3542F02D57EFCE9A6BD62C8FAB75CE39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F712265A78CB2524ABF9371BE2F3874D9D788471CB66B7D26E11C71E228
489B2.pygtex [26])
(./_minted-Tutorial/3A75E7306D7D2D81DE0C37038600A10A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/06DBC59F2EAD33E7A9518885378766159D788471CB66B7D26E11C71E228
489B2.pygtex) [27]
(./_minted-Tutorial/4393B8540CDD633A481E29B1CF252CE69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7F9F7641B195E2CACA3F77158DBE190C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/04626286E6AB345CB89BE7B7A049C3389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F2723D89FDBA794E82A8285BABB369CBEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [28])
(./_minted-Tutorial/64147FAF6F5C5028B073B3C809EE3E849D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DFDB859800920408E228736AD921B5DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D95D20C3283ADEDD76DAB3382BB1B0409D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AA99EB190DCB9061B7FD403ECDCEE4519D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F5B125A1E250BEBA411CA3B2BBF3EDDD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/39AA48793A64869F7458C1A2A0D69D2E9D788471CB66B7D26E11C71E228
489B2.pygtex [29])
(./_minted-Tutorial/29E9F3CE64EB99D132246C3633BA375C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/394CF49B3AAB621203EE87F2BD334CC49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3F2DB933A33BDAA3DB2299F2701B61CB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4307A980AB242F22FB1B0952E3FD37C09D788471CB66B7D26E11C71E228
489B2.pygtex)) [30] [31] (./Tutorial/chapter_seq_annot.tex
Chapter 4.

(./_minted-Tutorial/032C91EF2474FD3535629DC0CDABC8099D788471CB66B7D26E11C71E228
489B2.pygtex) [32]
(./_minted-Tutorial/28ED5ED993E569AC59FDA480CD731BBC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AD6AF21FB49ADADD3E9DF52EA341F92C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6A9404FB47549766BD16858F97A6D4079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B9321587EBA597104E435182128B200F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22FC566F5A2B47EFD3D63327C15F7FC29D788471CB66B7D26E11C71E228
489B2.pygtex [33])
(./_minted-Tutorial/510764EE0BB38AD6C688E71989677507EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/885E3C393ABBD6448EFA8A6D8D8498229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C60AA1EB70D11A096523A07FC1BD20859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7D4386614F3407AC9AFEDB894B0987D9EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [34])
(./_minted-Tutorial/B659A3B495F4BF5A9945B83B9A29DC2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/20D2783513E8123B155B9FE0B3FE7B4AEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/86FA506E88E30EB82E7186A57112C98C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D582F58715BB8D12B0A5A9CF9631A27C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C9D6C80CD8B460806CB6E7C2935EA6019D788471CB66B7D26E11C71E228
489B2.pygtex [35])
(./_minted-Tutorial/332D9C95CC14B124A8528A76F4917ECE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/925BCB3D0BD30380832BA5F2C6367AD99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D20F0AF7810B74883E42451F5810F9269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/47F0F8DD59EC4A71D5CA336E217F0C0D9D788471CB66B7D26E11C71E228
489B2.pygtex) [36] [37]
(./_minted-Tutorial/AD47AD29D6F7927F9406BE56096763889D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A89E686BA7930FBF8AE5CCC27E1AC5BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD11055284C1F524585846BFB03F6EE89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1C597DC49857D56C7E140B1D795218F39D788471CB66B7D26E11C71E228
489B2.pygtex [38])
(./_minted-Tutorial/EF871449F651FE5E7DFD84165065B14A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9ABE11BA111CDBEACB55DC5424AC66A19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D86C559003980DC8749AF92530435DFD9D788471CB66B7D26E11C71E228
489B2.pygtex) [39]
(./_minted-Tutorial/1C0A562378DEEE8E210765437B3E17009D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C7BB516F80A4A8F5C291ABDF3B6E0B499D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C737C9C2EF139AD4F965B3AC1FF72C759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/411A7DB0F7208D21C6099C86249233F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0C3ED75879971F09D72A92585654A32C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A4ED33BCBC94515EF1D3FF0CB0F2ACE99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1432CF672342B0A065BD2202A12E39209D788471CB66B7D26E11C71E228
489B2.pygtex [40])
(./_minted-Tutorial/3B61DDBFCC5B04C6BD9F6ED183CD312D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5039524AFDCC2184E0FA37B45448443D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/93B3AF8F7193FF3944CC29E4FE0F96899D788471CB66B7D26E11C71E228
489B2.pygtex [41])
(./_minted-Tutorial/B952BEC5DDC5176F8F8F8984196831F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D16AA28F327A9B07E6AE64737A6B23409D788471CB66B7D26E11C71E228
489B2.pygtex [42])
(./_minted-Tutorial/C08741A8063662E3CF1313052B7EA7A49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/83934A12FA213409ADDBED937D121BEB9D788471CB66B7D26E11C71E228
489B2.pygtex) [43]
(./_minted-Tutorial/7693A79AF1B5C3B342CEF51858B48A859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C59A3BD3577D6DA7BB95528A68C9B3119D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7FC68DDC3F22A92C79064A5F631D24579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E4EE1174D845FF0CABBFC735D0B5DF829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/890A92414EE9EE5FB3B2F7B834307EDF9D788471CB66B7D26E11C71E228
489B2.pygtex [44])
(./_minted-Tutorial/CC2666A1113601FF5DADD7ED2118A3FE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E29BCA3E51B6B75E0E5EFF17185016699D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D20811F7EAA2FB2ED0A37B2C0F1B24D49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E92A933EB86A743F11CDB887CD2A9C1B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/675833B93A69F5DE13F680548E25EA3E9D788471CB66B7D26E11C71E228
489B2.pygtex [45])
(./_minted-Tutorial/A8312A90F6B97A21EE1619F9A898ED369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68AB1E9E397375F82B6F3361E55900E79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/023FBCDB71B9572D8D436D0AA1193B639D788471CB66B7D26E11C71E228
489B2.pygtex [46])
(./_minted-Tutorial/1B29C13B779A89B3DE705BA0061B87939D788471CB66B7D26E11C71E228
489B2.pygtex)) [47] (./Tutorial/chapter_seqio.tex
Chapter 5.

(./_minted-Tutorial/3F38D5012926DD7C810DA2383F53D4989D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CE17C15EEBC1BDC9846A29B8188EB678D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [48])
(./_minted-Tutorial/357B0F655AFAF3808FD8EE23EE500954D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/480025795249845BAA7F48D4A45ADB219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F164035E9D5F8C01F84F5F95E2B166F1D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [49])
(./_minted-Tutorial/C82398A4A04383A063D2E64881123052D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1A4F5B10F895EA1A0898B313C8FE3AEDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/665A7700DAC7A651C288CFBC04910736EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [50]
(./_minted-Tutorial/3FC3FD6D12B3257730F3B4F11F7F82E9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/8C2F2A27559FC0864F47BBE543950C26EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/C1B7B447DBB266302BC82D7DBD162221D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3453EFD7B001ACCBD0126A13C98BAA4FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/23C65980427B41C7D9E32947CD41FD82D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36073AAEBADCD344208056C9868E001C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/32EC540B3F53C56F8F39A2A185A32CE69D788471CB66B7D26E11C71E228
489B2.pygtex [51])
(./_minted-Tutorial/3B09F0463D35461C42D2272763E73451D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/16EB556A216CBBE3D3F735350EA21A2AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F1A3FE258B41FCC45D4A8272B13EC395EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AD9EF2BC42CEF4E413923F9BFFE1BE07EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/58A82383AA9DEBBEEEC6694BA2DE777A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9562C263804C6DD613F075A435553A9F9D788471CB66B7D26E11C71E228
489B2.pygtex [52])
(./_minted-Tutorial/5654C63CA8B2C75821B4DD795E1D9C919D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1525A6F338DC70B7A056F15305A9579D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DCDC3EB1E5C136F423AC65A1907BE6B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/23394A4616015FFE4619934E984241789D788471CB66B7D26E11C71E228
489B2.pygtex [53])
(./_minted-Tutorial/48D36449ADA742065AC871DB512A14FF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7160C98DFF3E9F14B8FDC3EDEA5AAADE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E26B09583F35CC794E34E0D3C822C099D788471CB66B7D26E11C71E228
489B2.pygtex) [54]
(./_minted-Tutorial/A06B859656EACE1EB197B276B0CAD476D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/5B68AB5634E46F0A59E5C238174AC4F0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AAC02B6C28E92C88B051BB2DE451DBD8D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/FECB9DCFA3C63121DB586752E4215990EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/CC27A8BEB077BCA7346A8D13F39867D7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [55])
(./_minted-Tutorial/AE8667CEAACFF0F40839EE86774DD05DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/6467B5574DF68CEA13D016BEEC8841A4D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3D2A207C38AC647D99F5A8861A9D1AA6EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/DDD2E1D663317F4FFB7F8B7F03E4989F9D788471CB66B7D26E11C71E228
489B2.pygtex [56])
(./_minted-Tutorial/2EE890D1737C8A159C79BA4FCA81BB039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/77FD1FB1550DD72BE3E8CFAC5C21C7DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/022009B5C6117EE88C29BE7A45D87CF69D788471CB66B7D26E11C71E228
489B2.pygtex [57])
(./_minted-Tutorial/FE4CF732C73126A3874795838D95FAB59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7420F7622CCC097E8ADA484A405A3C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/07A24756D2FDD5E9B66DEB7412FC4D6ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7F04F15A8B73F26152ED44DB3C48528FEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/55430EAFE498E385842834603E0B8C86D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/47CA5358E0862EF3920CC2BF888DBDB8D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [58])
(./_minted-Tutorial/A50FCDC5880666D012F0A802072B4AC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D27A33312B4E81447304AAB2BAF2F6DCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/11D55B86CA819707A4B89E7FDA2E6E83EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/74E272C92C546FD61FA6D3DA5C1788939D788471CB66B7D26E11C71E228
489B2.pygtex) [59]
(./_minted-Tutorial/415024C641C8DA7A09117B3DFE240C789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/487DCC9F44A2539C9B32C0122AEF40659D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5098CD053449CEC3C9C30C90A007A3649D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EEEF4ABAD66CE989F67C9E27EEDE95CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F6AFF5A59B0706E4973BC1656FBD2D66D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/C4099CB0613585FCCD5EA7D8198704CE9D788471CB66B7D26E11C71E228
489B2.pygtex [60])
Overfull \hbox (9.93459pt too wide) in paragraph at lines 848--853
\OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org /
 pub / databases / uniprot / current _ release / knowledgebase / complete /

(./_minted-Tutorial/D52DA4EEEEE2BF0FBE89EE253714929D9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (4.48064pt too wide) in paragraph at lines 891--894
[]\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u
p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1
/cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/D41A88D88AB398F0C3B719A5C7D017C141CFBAB8D39E8FFAF3C5D885168
6F649.pygtex [61])
(./_minted-Tutorial/B4D970E8C81930851D8639D77EC3E41041CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/7C4E0944FB13EC4E75DD6FC64900395A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C68CC3C9B3A505FB972706356D7F336F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/61AD507889ED86CFCEFC880BAF2A27779D788471CB66B7D26E11C71E228
489B2.pygtex) [62]
(./_minted-Tutorial/DC5117490176932EFB8A7F0E0DA450F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/657D43328835FC01F9133F8BC964475D41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/82CBCD9B9F23373D67D9D0D7D2CA363F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36F8D0FD2B4ADF57AC4203A0C80C64719D788471CB66B7D26E11C71E228
489B2.pygtex) [63]
(./_minted-Tutorial/9CEF7BF9B2634ACBC930BA5EB6DD7342D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [64])
(./_minted-Tutorial/AC02E3950380715FC960C04EF317D69FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1C65F538FA7F22F7BB5183FC1553A0C6EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/935F773BF84C3BF326F4BA093FEC79D4EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [65])
(./_minted-Tutorial/C194E2231D844AE7D0223173D2A89991D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/10CB116B7358444BA68AFA046B5B84D5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/29D12D495374A5A8C37AEB7083851DEA9D788471CB66B7D26E11C71E228
489B2.pygtex) [66]
(./_minted-Tutorial/920133226A22EEB682D854077D7FB78F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4EBA0A67E686E73FAA1A0EB27C2600289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C06224D76A18C126B27DFE55444AA3FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E381FF526AC999B71717F178C997F6B29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F05AD4A17978E60C531612707D8F26A9D788471CB66B7D26E11C71E228
489B2.pygtex) [67]
(./_minted-Tutorial/D19467E367634413AE9EE17A62E5D9EAD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/EDF3737891061C33EDE0FBFD16CCC63BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D1EAD55A1F8AD3DEAB82383A4F020F53D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
Overfull \hbox (19.46596pt too wide) in paragraph at lines 1349--1351
\OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) 
[]\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm
tt/m/n/10 SeqRecord.format(...)
[68]
(./_minted-Tutorial/2F337ECD1F936D416FF9C5C6F41A02D79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3337CD054623BAC21B6021E996EE0DFDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
Overfull \hbox (21.32593pt too wide) in paragraph at lines 1393--1397
[]\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm
tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt
/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/D3AF6542680CA390CDA8C8DF87C693D39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D749A84299CF58E876E9A899069830DBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)) [69] (./Tutorial/chapter_align.tex
Chapter 6.

(./_minted-Tutorial/9CC7A6864E21FFDDB3F4D02F2870DF42EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [70])
(./_minted-Tutorial/81FAFBAECB3A03B11080ECF19D4CCC809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/31E7567531B3A1035700A1E555A47FC09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D2523B56ECD3F392CD3E37EEBE302AEC9D788471CB66B7D26E11C71E228
489B2.pygtex [71])
(./_minted-Tutorial/AC12821BA0AEE8F48238EAC359A310779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A6D29782988E1FB75F30F2D60AB93C4E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E48647CD11476AB33349258EA43C50F2EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [72]
(./_minted-Tutorial/16CCFD1DA7A71D5F6D9A86870C5604079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0B89B536EECC0E9CC886A8B4CC9713E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EE5558D4A829B63692DC55F8215FD331EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/FA669D1E3279749AAAA27A72F3B44533EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [73])
(./_minted-Tutorial/9119ACDDD7EFFD39008E7F98AB7BF7569D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C54BE5D00F2871BB58E36C383B3B4DEEF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [74]
(./_minted-Tutorial/CE4E385956165A535376F6D73447D3F79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F55715342346472744E837C465922E6EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/1B5E788850B45798FCA06125D5880A14EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/B913EFE8AC0AC995AF3DCCAC856FF020EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [75])
(./_minted-Tutorial/5F9DFDCFBF42A04D6BD31E8E9638DA579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BDB62F4C6418AA14588B7DBEA69D61C5EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [76]
(./_minted-Tutorial/A8D0C008D3D8E2CB96D91B2A5FF2D3189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9458BC75C22971F0F7F09C79C7D6AFE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FEF99AFE39529F3F1A5EFC7A23714477EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [77])
Overfull \hbox (5.54102pt too wide) in paragraph at lines 434--435
\OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t
or/iterator. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()

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

(./_minted-Tutorial/9776F24C4F96F850E549BEF997E4D18C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8256B42DA32121F3B83617DD03F40249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DA108466F70572EEAE2D54AEA4C156A19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8FD10ACD641F4427B35E96F33B44479FEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [78])
(./_minted-Tutorial/ACC9FF1F2F025F77815D96DC3115B7DF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E530BB128C8AE6BCF7BCE91DD4AF189EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/C17F8CD5F33DB6EB328532E02ADD1FE69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C02EB78C9555A4FEE4954D77162ACF99EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [79])
(./_minted-Tutorial/74D8F602592BD3646F12A04951B2C44C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB14E2060AF38515C129AB5808537F16D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E78F5A80C222A5B2777910FED4F43F56EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [80])
(./_minted-Tutorial/4D0AF4A40C449D27FF181EC477C63CE69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2590B11C695B984E246A0A91734F786C9D788471CB66B7D26E11C71E228
489B2.pygtex) [81]
(./_minted-Tutorial/508710FC1759BFFED598544DEC99BC0D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/886094CE2C1CAC714387144709D5A47A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6DC12DBE1D4FD44E7395C66258B5EAC99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CAC16111FAD8C2E739F6D7C04A986BF09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A4149E9BEF55B5853014A59A3CBBFBE59D788471CB66B7D26E11C71E228
489B2.pygtex [82])
(./_minted-Tutorial/8327145320A3BCB412D977F6683B71A29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E096B06E33D157FFE18E045579F838C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C7331D522D75BB7830A1364BC3B716929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C45FE25766D82D1C4A245CBB9A77DB009D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C0937EED558D842CEA8E3DB9514C6E599D788471CB66B7D26E11C71E228
489B2.pygtex [83])
(./_minted-Tutorial/8EC03E9C8500D05C6439AC85123A92539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AE857C14E4731CC6F6EBA530514600979D788471CB66B7D26E11C71E228
489B2.pygtex) [84]
(./_minted-Tutorial/F88E003F9A4A95A929AA549FA710239C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/523928538FA511A925EC995B1803BD169D788471CB66B7D26E11C71E228
489B2.pygtex) [85]
(./_minted-Tutorial/CD47D1913C82182C164BD47DA47152829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7AA94166BAA5F4CBB44EF4336F3E8939D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B49F47BF4F2EB4093BDE51E631C630649D788471CB66B7D26E11C71E228
489B2.pygtex) [86]
(./_minted-Tutorial/230B4706E315BD2F2A44F2EBCB37A4429D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C11A66992B6C74B61F5A0BE7757AF3BC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EAE190D91CC491562308EE568F9863689D788471CB66B7D26E11C71E228
489B2.pygtex [87])
(./_minted-Tutorial/6256254C5A7DFD21185291C77133BFDF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FC96AF22EDD72BC4AC2EE47EBAA6B0459D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E941CFC951CAE25312D9A5CAC9B274259D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (8.40039pt too wide) in paragraph at lines 1126--1130
[]\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi
le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO

(./_minted-Tutorial/EA6A02999040945446E72AC6A00E56D89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/106ED62B0CFC10E7D5BC6CFC9CE003BD9D788471CB66B7D26E11C71E228
489B2.pygtex [88])
(./_minted-Tutorial/4D75AC9EDD74C466535F1EC4944833F79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/14F1F3BAF80772F5999B0773C02432E79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A261B9E9E2D4EB3C1DF5131C6F7399989D788471CB66B7D26E11C71E228
489B2.pygtex [89])
(./_minted-Tutorial/E2B86D066966C8BA13EEEF614D3E74549D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E87BDA1F176DA567A757DBA0231BC5BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6BF1884F2D94AF8D067A2A20A9A41E2C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F551ABCEBB0043257A807C76B9D81B5C9D788471CB66B7D26E11C71E228
489B2.pygtex [90])
(./_minted-Tutorial/37B6E52C66902FA821D4B0E80172CE749D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BA045AD7DFE0F0F3DD972F3E2C40BA19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/482576AF06E80D82290535FF7857A2409D788471CB66B7D26E11C71E228
489B2.pygtex) [91]
(./_minted-Tutorial/5D3CCD84BC2EC46BF5FD98E7A3FC7266EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/D9565472E525C9F2B734FC37A70D258EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/39152F199CEBB3375366F2E9478245199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/256B036DA9C3EDBC9EE41E2E52FDE1AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DC6CF8B5CDDD2C32E2052C03AF3856749D788471CB66B7D26E11C71E228
489B2.pygtex [92])
(./_minted-Tutorial/CEE035FF629B69F7D6B6351C1DCE24939D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DF151703751D72BD556402B910190A879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/004029547AAB1172AF2684D2CA89EA889D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/554024580088332FAF0EA9296BACE82E9D788471CB66B7D26E11C71E228
489B2.pygtex) [93]
(./_minted-Tutorial/419ECEB266819C8DCC38EB3E1DC3E3619D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/143B9D317680E51D3A6E5641208720CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6CCC707502EDD92E9C355854215BF8859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0A4B1939051DE630E53C7151447C8DD49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2B6197C314840AD3EC15C56F366120C59D788471CB66B7D26E11C71E228
489B2.pygtex [94])
(./_minted-Tutorial/E5E00F47BD7A0C8BC5F88185262838689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/52B42D5819C8EC5D57A21AE60D28F6CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F566D907B2F88621EC4175F1F17AE049D788471CB66B7D26E11C71E228
489B2.pygtex) [95]
(./_minted-Tutorial/0FE96E337A3BA73D52896D46E2E233DC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/434D41043E1630324FA64E8B55B90BD59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/48453D528762FF183499778647AF218B9D788471CB66B7D26E11C71E228
489B2.pygtex [96])
(./_minted-Tutorial/BD86EE3248811DE8FD9DE8ED02397A399D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (76.42714pt too wide) in paragraph at lines 1707--1711
[]\OT1/cmr/m/n/10 By de-fault, [][]\OT1/cmtt/m/n/10 aligner.substitution_matrix
 []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 None[]\OT1/cmr/m/n/10 . The at-tribu
tes [][]\OT1/cmtt/m/n/10 aligner.match_score []\OT1/cmr/m/n/10 and [][]\OT1/cmt
t/m/n/10 aligner.mismatch_score

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

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


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

(./_minted-Tutorial/DCCEE6D592009E7B8E7DE81563D8D4CE9D788471CB66B7D26E11C71E228
489B2.pygtex [97]) [98] [99]
(./_minted-Tutorial/98D9A5E0CD47E306CA0DA2AFE878514A9D788471CB66B7D26E11C71E228
489B2.pygtex) [100]
(./_minted-Tutorial/FBB2100548FA74FADE3EAE28A2DE19119D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C9DFA2EBF75572BAC340EC89D69B3D49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B788F0FBC120E74A47922EA232EB86719D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/504D01562B8D0E8E16B44A19B5FCD5EF9D788471CB66B7D26E11C71E228
489B2.pygtex [101])
(./_minted-Tutorial/DE91DA6F7C30BDD779CED0A91AB75DAF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A59C6CF4854355E98CC312686998A38B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D37B0AE7B982968C1F24FD3EAA535EB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5214A9AAFC8A40430707E3A6B6DC0D019D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/32985CB8E0884A44019C3AD3006E3F9F9D788471CB66B7D26E11C71E228
489B2.pygtex [102])
(./_minted-Tutorial/0758643069FF669538B9540ECD26C94C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BDC838410673E955B3534CCCB8AC77F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/385490B66B3AC742DD6257196C784FE29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BF27E9BF2471340998870C4A342965929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A072B421EFC519E90AA0A540338E8E4E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C5780017603AFBC3BB3E9F52ED6688C5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/76E331C5187C259B69198E91FC4AD1129D788471CB66B7D26E11C71E228
489B2.pygtex [103])
(./_minted-Tutorial/BF7EA4D0E316F88B3A609CF62C6CD3579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A564D138D2F52B4E2858B9D14814966B9D788471CB66B7D26E11C71E228
489B2.pygtex [104])
(./_minted-Tutorial/68A0723415861BAD8A4809FC33D4A2EE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/66AABFA387595237A8CE2518915213F89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B15E737F9393063B641148640673D9919D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EB25FB90F1A09B5CEE3428AFC4487B469D788471CB66B7D26E11C71E228
489B2.pygtex [105])
(./_minted-Tutorial/EACCEA5889A222FB9830265E6A8DACB99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/874975627BAB24A36A35FD4C633D246D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/35E64D230C4D7DA7362D8F8BA278ABB59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B0937117DDA6BB67D133C99E550AD5BD9D788471CB66B7D26E11C71E228
489B2.pygtex [106])
(./_minted-Tutorial/9C81CE609C3C74FF6DDE53A3528FDA3A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AF515AF157FE4840A244030AD4DCE3A79D788471CB66B7D26E11C71E228
489B2.pygtex [107])
(./_minted-Tutorial/C8046F75BC00F97BFBB444E7FCFDE7BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9249A0A01E1025FA8711414C0E36841F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D1BAA37DF09A601FA4C6F2BEF162C3E09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/52868B2F44504455E4969FEF2614B63B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/433C9892AE287F36B57A8A95FE75AB949D788471CB66B7D26E11C71E228
489B2.pygtex) [108]
(./_minted-Tutorial/E7E68A8851DEEE300947A0531513417D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/60C347B45B5A049CB5B00A20D29DEF659D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1498327D070D6F98AC2E3DB39EAA17339D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6502BA65433924876427DBB6013C10039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE6EBD36098288038E8FFA4A045EC8FD9D788471CB66B7D26E11C71E228
489B2.pygtex [109])
(./_minted-Tutorial/B66E52A450DAB10C11EF0A5303F7F66E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8791CE2DDF360A2EB13DED7B355F10129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/ED55B2BAF04247D4F10E951590AA50779D788471CB66B7D26E11C71E228
489B2.pygtex [110])
(./_minted-Tutorial/779C61444C54C1736794F4E11B0E326D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9FF41FE72E025C3EC8E41470B268E1059D788471CB66B7D26E11C71E228
489B2.pygtex [111])
(./_minted-Tutorial/779CE460F4F768A71E6F35DDB7FDFA779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9EF49B98A62C70CD81126514DF7966009D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (19.80069pt too wide) in paragraph at lines 2612--2613
\OT1/cmr/m/n/10 In this ex-am-ple, the to-tal num-ber of op-ti-mal align-ments 
is huge (more than $4 \OMS/cmsy/m/n/10 ^^B \OT1/cmr/m/n/10 10[]$), and call-ing
 [][]\OT1/cmtt/m/n/10 len(alignments)

(./_minted-Tutorial/F89522EF58FB067C6521C367C71347169D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/76A8D90A1791A7B42DD5E6329FCCBE209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/399250FB2BC395588B8004ACD928BE9C9D788471CB66B7D26E11C71E228
489B2.pygtex [112])
(./_minted-Tutorial/882BD2544386DECA236BF25C7DD648579D788471CB66B7D26E11C71E228
489B2.pygtex [113])
(./_minted-Tutorial/22FCA15B328DDB0383F97012E3C1FA709D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DA98355B1CF48169F9C82F2DD1F86A299D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/13D646E6B49807044DBDC43707A098469D788471CB66B7D26E11C71E228
489B2.pygtex [114])
(./_minted-Tutorial/467CA50C36874E405E988587FEC076869D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E4398C5237FE7113BC5A8DE3B0E138A69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E827958137C7E69DAEDB0C4151298E629D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A94C18D2207C354646F831D57FD85B359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/801A90831A5799E3FF1FC0A5E721F4F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4329189CC201D756D0770BD7596DF0D89D788471CB66B7D26E11C71E228
489B2.pygtex [115])
(./_minted-Tutorial/C7C0911CDDC1913791B1BD1EDA0EC55F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F13283947C7FDCA9456A70797E029A739D788471CB66B7D26E11C71E228
489B2.pygtex [116])
(./_minted-Tutorial/AAF53200644F4F68779FB844730087D39D788471CB66B7D26E11C71E228
489B2.pygtex [117])
(./_minted-Tutorial/FCBF8AC8128D86DFE3607A8465EC034B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/96A1DC106863D5F4D96B9200B7B5BE069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7323803F0E90CDA6FB16D10E868318BB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FBFC10402209A281F117C1A7C3D2057D9D788471CB66B7D26E11C71E228
489B2.pygtex [118])
(./_minted-Tutorial/04CF4E50F88DE1F6947064E1188A1BAB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/88E3C6FE8CD1E52180656649B61F8CBB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3352A1628AB7C0D638BB368952D0DEDC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/842D73F66680850822D006857AE71FE79D788471CB66B7D26E11C71E228
489B2.pygtex) [119]
(./_minted-Tutorial/FAF36BBB1FEE777074E1CB3B06F18C8A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6B4057929CCF1526CF34FF943CFE31359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E0AB5DB602ED615A4FA228E22B0CC4F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5E9D6563DE4DEF6BBF8840F7693212F49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7C466424D72F09AE5AACA884161416F99D788471CB66B7D26E11C71E228
489B2.pygtex [120])
(./_minted-Tutorial/F3DBACE95BC0B45F9EEF5BC8C67DEB0A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CC9E9C07C5DC6BDB4071B2A0EA8252789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/55D34AF6272FC77B12E7D4DD16884A6B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A5A764AD6E5C1A70216D27249F6800939D788471CB66B7D26E11C71E228
489B2.pygtex [121])
(./_minted-Tutorial/54EF0A3F068FF357EC3C51C6E1172A579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E78F0FD7A0E228935EE2D650C9315EC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CEB2F5A09DE2611D752331C16E5BE61F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/007A62C4B86AFB9385A7D862416647079D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E19493E35A1B212412F37B3A7079D5AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B051755682044B54FDC8CE728FD23B5EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [122])
(./_minted-Tutorial/659317FF2415828FBE0F4505ECB5B4E59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/60D893638743BD147116D13E00593D6C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FC6687367D9EC6B1C018CE84CA30555DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [123])
(./_minted-Tutorial/9AD9216297281F0858F16EA5C03B98AF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB8FA536E934FA2DC233E7FF52DEAED49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/14104DE21243051DA2E8D004C5D1A9ED9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3C42B04C08C3B07CABB6D2D7AE1F1B6D9D788471CB66B7D26E11C71E228
489B2.pygtex [124])
(./_minted-Tutorial/A6E4A89F3F3E07605D5B2BD57C7671CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1795B10D0BABDD4E83A8B6EBE5DAF8CD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/691C9A3D9A1EB52FAECF7E4C91F03BE99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9A7868CC2484B4CFB34F94E7549F25199D788471CB66B7D26E11C71E228
489B2.pygtex) (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)
(./_minted-Tutorial/A7706714F4982C826867A73C2B665ED09D788471CB66B7D26E11C71E228
489B2.pygtex) [125]
(./_minted-Tutorial/44E2C06C8661B128385CD75A7E7608AA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F120EF3444F3192D48657B4E524070179D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9AC50DD22A56E4DC2B26465D89DE35EA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CFB7E0A19AF729834746B283E60F20919D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7DA73F8FE9E6D95C2255220886791B5D9D788471CB66B7D26E11C71E228
489B2.pygtex [126])
(./_minted-Tutorial/E9F207F5DA488246642864EBF9EA466D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/15FD2886E49804AE97038F2733592C719D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1D1D98CF394058EA9EB8F6FA3B0DB75A9D788471CB66B7D26E11C71E228
489B2.pygtex [127])) [128] (./Tutorial/chapter_blast.tex
Chapter 7.

Overfull \hbox (5.71313pt too wide) in paragraph at lines 45--46
[]\OT1/cmr/m/n/10 NCBI guide-lines, from [][]$\OT1/cmtt/m/n/10 https : / / blas
t . ncbi . nlm . nih . gov / Blast . cgi ? CMD = Web & PAGE _ TYPE = BlastDocs 
&
[129]
(./_minted-Tutorial/A6D333F851BCB09A0C02030C1BC37AB19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/69F91830197D9990EA9A0BD7D074EE219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/00F087159F0534545C0B7288838BEF0E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8A150C3E431DF572EF74B2B19AB15AF89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2FDF7B3FB3DC9B4B3C157122F78C3F4E9D788471CB66B7D26E11C71E228
489B2.pygtex [130])
(./_minted-Tutorial/0E750E34F5C53FAE26988AF1CDC7FBC69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C2049D788471CB66B7D26E11C71E228
489B2.pygtex) [131]
(./_minted-Tutorial/21FCFA3232935EE0DF07988BE50D1AEF41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/88BD5D9B190061FD4FD34D2573EE47929D788471CB66B7D26E11C71E228
489B2.pygtex) [132]
(./_minted-Tutorial/CF5D749C3878C5A1FD3C8C63CA51FD089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C9558BD802C8764E46CF73625C14C2049D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E34865BFB20F9D165069B84AE52180049D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E0F63513A18DD0126288BC98B9F403949D788471CB66B7D26E11C71E228
489B2.pygtex [133])
(./_minted-Tutorial/A614B982013DB6EC38FCADD82303A8BE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DD49CD888784736545A3066AC257FBFF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B7DE908D2BB5BA4FD1BB179810D8D2389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/16EEC09BFB431080BCE9C5E6ADA5DAA99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68259DF5B1930070C029D5A72D891A369D788471CB66B7D26E11C71E228
489B2.pygtex [134])
(./_minted-Tutorial/0C1E2B9A587BB44A7E19E83A4E5B1924EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.

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

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

(./_minted-Tutorial/6D0EADF658E662CBA394834EFAC7346EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [138]
Overfull \hbox (2.9019pt too wide) in paragraph at lines 85--93
[][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle 
con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10
 HSPFragment

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

(./_minted-Tutorial/0EF47CD31A1F702FF10BD5C95E6D18FC9D788471CB66B7D26E11C71E228
489B2.pygtex [139])
(./_minted-Tutorial/BCDD1F95C8585B3C70DE9C1280B519559D788471CB66B7D26E11C71E228
489B2.pygtex [140])
(./_minted-Tutorial/7A12FEF8445FE62A62C651C8B4EC163F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/362861C831165FEA5413E0240053CD899D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/40227DD719AAD22E8DC2923BF43CE3279D788471CB66B7D26E11C71E228
489B2.pygtex [141])
(./_minted-Tutorial/FD9C81C098491598DBFB6208173BB5759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/87D36F7AE3CBC4EDC6FCCFDE0173412C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CA24D00985B075C56E7C71A246E439FF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE8A481953AA0F7BD7A99C0E281AD1A09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7AA701BE1D007CE77D402E8CBFC777A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/906546E8B6F7831A0E7C5FC93AA56A039D788471CB66B7D26E11C71E228
489B2.pygtex) [142]
(./_minted-Tutorial/0B914838010D3E86EC368E1702EB72539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E4688DCAB619DBEB784ED0D836D1E6199D788471CB66B7D26E11C71E228
489B2.pygtex [143])
(./_minted-Tutorial/DDECA9EB99D9FA38003A52C1765930729D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/578CBF904F35965EECFEC1FA694F07529D788471CB66B7D26E11C71E228
489B2.pygtex [144])
(./_minted-Tutorial/C0EB7D270F64704BA5AF848A21AACD649D788471CB66B7D26E11C71E228
489B2.pygtex) [145]
(./_minted-Tutorial/84848AABE250EF05E85067B2CD3275B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A2EA3A12F7596A64ECEE374A9C53499A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E7A6E47CCC64E8FADF02D1CDC62468639D788471CB66B7D26E11C71E228
489B2.pygtex) [146]
(./_minted-Tutorial/A3385B945E43CC076FFA693B27681F059D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DAAFD2AAF126ED8D7284764B561B5E2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4B4824DE2ED3215F02082987EE5735779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/61406D58E5F7C40FD0A0280DCAA66B469D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BF77764978D907008BC936FD2A5FCD959D788471CB66B7D26E11C71E228
489B2.pygtex [147])
(./_minted-Tutorial/CE618F26D70602D511E57E53CD8804449D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE23F71CD74CF7717D38AD01C1E1C7879D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (27.24287pt too wide) in paragraph at lines 743--745
[]\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10
 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr
/m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment

(./_minted-Tutorial/338C616C7128C3DB7FFD516F5C2BDA129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1195D6861E887568107FA7F463EA9BBA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/31F43A46088F6D2E63B39857A35369099D788471CB66B7D26E11C71E228
489B2.pygtex [148])
(./_minted-Tutorial/16771935702D6A2A9762A80A621013D89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/046FE550C51B323D1E952A27E126FE199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A55E467518B2E0F936A232F0970B10379D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6D69D310788199FBA6E8A5BF5CAB20219D788471CB66B7D26E11C71E228
489B2.pygtex [149])
(./_minted-Tutorial/2C71B4AE1F4F9990447491C6C291ABC29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD7ECFDD9D017B829A54C995FEE42EED9D788471CB66B7D26E11C71E228
489B2.pygtex [150])
(./_minted-Tutorial/3AD8335853E972C8E62AAF79CF0A3D339D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/758BAC7574A59544686354199D20892C9D788471CB66B7D26E11C71E228
489B2.pygtex) [151]
(./_minted-Tutorial/7A63CB5E786CCE052981F7DD10653DA99D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (14.20721pt too wide) in paragraph at lines 1055--1059
\OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT
1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like 
[][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 ,

(./_minted-Tutorial/DC4E434DA5B851CF1E22BD3608A311F49D788471CB66B7D26E11C71E228
489B2.pygtex) [152]
Overfull \hbox (20.13245pt too wide) in paragraph at lines 1087--1092
[]\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us
-ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt
/m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/0AB25750C7D89E832295045C60D6B8C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DFACFE04880AE0CA2E8E32ABDC9E98689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/51F256FC56FFFAE1F1E84A4EFC5BAE559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5BCEFFE3DBB7A0AE4FD5D950731D72DE9D788471CB66B7D26E11C71E228
489B2.pygtex) [153]
Overfull \hbox (11.82602pt too wide) in paragraph at lines 1167--1170
[]\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 
also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic
h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse

(./_minted-Tutorial/BDE985FA3ADA6B0D37013C3D5F37C1769D788471CB66B7D26E11C71E228
489B2.pygtex)) [154] (./Tutorial/chapter_entrez.tex
Chapter 9.
[155]
(./_minted-Tutorial/95F72AA1E59C898262005610BC25A6BA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/320E9A38F759168BA03B078BD9CC013B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DAEC2235DDE454C09ECEB0DF4CD26FB59D788471CB66B7D26E11C71E228
489B2.pygtex) [156]
(./_minted-Tutorial/7692669934D8ED6DEE1B8B66847454219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4E8E7490F3E1B9120A0B1B53C024FA369D788471CB66B7D26E11C71E228
489B2.pygtex [157])
(./_minted-Tutorial/C21F612C84412948C9890ED976F536B09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E05622F86D5C6456282864B1095B19C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/846A93AAA063B5CBA3EDEF3D5FC8C0089D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/03DD15474BC34E37527B593FC22220FC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B7AA3167A6472C6C33ACA91F8E88FAC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/82DFC9B19D35F2D9482DE6B365FC35F69D788471CB66B7D26E11C71E228
489B2.pygtex [158])
(./_minted-Tutorial/01D9FCC3424FD0B497241E81D2FE83C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F74B27B285F0D0CC7E69CABE07232C689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/83C7791C8A9F82BA61AD4B1644D502779D788471CB66B7D26E11C71E228
489B2.pygtex) [159]
(./_minted-Tutorial/3B6409EA2F4B25B8F136CE97DC95E8C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/53F668B0CE9069489F6D35B114D072B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/49E5F2A1DFC2444E5A673AD6C6E3F19F9D788471CB66B7D26E11C71E228
489B2.pygtex) [160]
(./_minted-Tutorial/96245EB54DC7A4475CD270566892BAE49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AA26452EC447FD01D35D14B1CE4F31479D788471CB66B7D26E11C71E228
489B2.pygtex [161] [162])
(./_minted-Tutorial/042DA7A7135DAEF797FB2EE6170C3B6D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/11417087354B0B78128E27B0162F48D5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [163])
(./_minted-Tutorial/51CC2C09DB95235CA19612EAFF65F4879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/01919CABECEE21D3FA5A6B7A01CCCB5E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0DD80468D8C175A94BC63142BD16EF1D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/414E52C4377A1D0E6A428B032A7756FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6109D29005C5EC9FAE01CDFBE62EF0089D788471CB66B7D26E11C71E228
489B2.pygtex [164])
(./_minted-Tutorial/A0ED7F47BA117071BA21263E7AF6DB279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3C5A1B892E98E1E6E8C179B5F465500A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/68622353B578A611D2F621023E3C4BD19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7455566FBE10CCFD5236DF65992A9F709D788471CB66B7D26E11C71E228
489B2.pygtex [165])
(./_minted-Tutorial/6E7EC19AB4E894FD7BECB47DC082FC389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E02371BEF7596435E8F90267E0362E0941CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/8A1D9304F979E03817FD393E44DC722A9D788471CB66B7D26E11C71E228
489B2.pygtex [166])
(./_minted-Tutorial/2B17732B358EE5D871A248019977CF38EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/2186E927D5A018F8950E8A7D0F734E71EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/DDE0AA7C839DD601590297B5D523D03B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1516062A6E16A043D5996183E67DEB86EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [167]
(./_minted-Tutorial/08B5AC3C9DEAD2E377FE070B35391F0B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/898885F88FEAC697F30E8E063D95F24DEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/8BFD5A5D2A0A2DB21DA15E3F1719D3F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B89E703729CE0DB5EB3456180292FA1BEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [168])
(./_minted-Tutorial/06D29A54CBCE7E9BEC9B02AF3737953F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/115C0D8716DAB358EAFF936486F27AB99D788471CB66B7D26E11C71E228
489B2.pygtex) [169]
(./_minted-Tutorial/9BFD2F013E1A1D8756C2BFF5B3706AADEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/9D66917D850D2EF232ECFE32D0F8D1CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/474ACCF7269CF6DA8C1148E094B63C809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/265BCBE09451F85D4BB86E81E6F3D4E19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/077B6C28FFFD9E8EB72387BF7F1D9BF19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/41118C19A2E462F9721E8AB1E52AAFC39D788471CB66B7D26E11C71E228
489B2.pygtex [170])
(./_minted-Tutorial/8D1D071E3CA3DD9187A6F2C35836C58A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E297F3C90950B761CCB974F597BCC129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/30DFAED5DDA7DA75BB6A3BF0F0C12D759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E07A958FADB74CD60F7086FF6319E2779D788471CB66B7D26E11C71E228
489B2.pygtex) [171]
(./_minted-Tutorial/55E8C5FCC00AEE8A4E1D892ACA95C2BC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/473B4163A14D626D6B7A08A26A0A12669D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4802D221A3EBE7AAC3E07CB05144CA279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F7C9857DB48F3111F31BB49EC39F2019EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [172])
(./_minted-Tutorial/650077A39F2D52831A52D045B184B6249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/17E5085C64881C08DC82C2B5573291F29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/076325C16F7C56460228C73B3147DF7AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/2018A02508D4B36EF0217BE478D18CE19D788471CB66B7D26E11C71E228
489B2.pygtex) [173]
(./_minted-Tutorial/67F7BC27D166185C4B7B9A9F270ACDA59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F01452391D049758B3588D8F37184AA1D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/04D54F815C5EFA53EF9010776D1AA07E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D46819E08D3CDD954897218A7EB7C8C09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57648E2674FE9BB727770109CA65C71A9D788471CB66B7D26E11C71E228
489B2.pygtex [174])
(./_minted-Tutorial/676B968CE2CF2F3AEF6899757E020B1E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8778F0F3798A99FE0C3840234CAC2B5B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FAD1D32BBD3E6FC5FE31DBBF8029928A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/85AA5F6E67E515A70F5F0A4D9A0548C0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/24D6870F7CF00B7F93EF1F55424D4AD09D788471CB66B7D26E11C71E228
489B2.pygtex) [175]
(./_minted-Tutorial/964257041BEB9E732FF9A943209BD6ED9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/600193D5D5D44162E61A3CAB404484269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E963D1B8D3330FC994CC39110B6420389D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/574A29DDA761C1725F490FB0F1CD4EEF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6FD15C01D270A661A77854FF78F033B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5845916CE276A61945EF5849B982E8A09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8905908F46BA67CB99A3360F253875C59D788471CB66B7D26E11C71E228
489B2.pygtex [176])
(./_minted-Tutorial/4DA8ECCF1EA4588537B571B9F46E13A19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/714497BD693AE1BF76AD1C44D3A43F2F9D788471CB66B7D26E11C71E228
489B2.pygtex [177])
(./_minted-Tutorial/824F6600A92AA40841D5D9A4C2EDC5FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3EC6E0F9D852E0B8DED607938A727979D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E8FC03C2B925F09D2849BD1DDCBB38489D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A137A30778671FFE0F193EED7A8819D79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D76169664531538D144C55FFC33571B9D788471CB66B7D26E11C71E228
489B2.pygtex [178])
(./_minted-Tutorial/D49E38D9D1357F6225DB42AC5AD5ED7E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CC6CFA7B6751FFF8C74660FCC40D3C459D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0D86B77B8C40BC4335F18EE35CB936499D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/37575ADC7CF832C14B5854633F9C88D89D788471CB66B7D26E11C71E228
489B2.pygtex) [179]
(./_minted-Tutorial/5E81FD2679BB8BC4F82244B31C22C4779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7212F8F4D805E6009D8612AB61498E249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B038E9BC100BB2A231E2B4BF11B0330C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3256378680D2E01A0D283817FC4F96339D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1E93113A22D275DCF1ED22A91F77D574D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [180])
(./_minted-Tutorial/4F9D9C998FB1DECE2FBF932B39921FFAD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [181])
(./_minted-Tutorial/43EC7DBFBCAE4E8B197BA170F7FE7CB29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F55F80E3D84EDCE0B63B5BCEC4E927A9D788471CB66B7D26E11C71E228
489B2.pygtex)) [182] (./Tutorial/chapter_uniprot.tex
Chapter 10.

(./_minted-Tutorial/DC3FD651AB93A0CE9D668FE4206D1A869D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DD1C7AE6EB54A3133F3D58EE95B3A6689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BB844FCBFB442A424E4ED0D244DD67689D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/930B60BD569CAAF368B0E614553F30309D788471CB66B7D26E11C71E228
489B2.pygtex) [183]
(./_minted-Tutorial/ADCE00FC778B0EA886D44F1AA65191829D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D3E040F0C8AAE9BF46C3D89DB9346699D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C65ED72167AAF5D5730D19463FD692289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CFBCB7DFF63857026EF72107C91C4D149D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D965DDAA766509A8449374C475416C069D788471CB66B7D26E11C71E228
489B2.pygtex [184])
(./_minted-Tutorial/747E2FE5A2594F5385BB7437A45179189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8837CDE38481CF679BB33997916F09AB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E15781AA166AC63C2DF3BCF25628224EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [185])
(./_minted-Tutorial/956383F4066B9E093C9D2E3843CA02209D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BA8B23CD43F97133B0CE8ECD0A9462AAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/8B296BCFBFAA7137B45E8CB899424BE49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C2EF087C5641CFFF6A40A4396FE9307B9D788471CB66B7D26E11C71E228
489B2.pygtex [186])
(./_minted-Tutorial/9AB12EEC55BEE868B932EF7EF12109CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6E2B75EC45BA35CA8C7799FFAFE69A4D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1DE080CE5283B4D334F81719880190E29D788471CB66B7D26E11C71E228
489B2.pygtex) [187]
(./_minted-Tutorial/6ED198EEC186F92A098C5692A874CF5BEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/F4AB180AFE85CC09CE3F73EE547FC7839D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B1A88EF3A17DB1FA7EC5A60B27A37BF99D788471CB66B7D26E11C71E228
489B2.pygtex [188])
(./_minted-Tutorial/454E46BC171F751C15F6A295F2284AB79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8DCADA174B7DBC35827913027E1507B49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/20DD2D91201FBA08EE81FE73D557B6229D788471CB66B7D26E11C71E228
489B2.pygtex [189])
Overfull \hbox (24.29903pt too wide) in paragraph at lines 365--366
[]\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n
/10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/
m/n/10 SwissProt.read(handle)

(./_minted-Tutorial/30A3D5D1EA4F73DD0984EDFDDAF9090C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/950511DA0658C1A2824DF92F06F34BE89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6A833CD3DDDD6A4CCF169D082C63D87D9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (65.93893pt too wide) in paragraph at lines 409--410
[]\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m
en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re
cord

(./_minted-Tutorial/DF2DA17EFC0F6336210C74066809B7539D788471CB66B7D26E11C71E228
489B2.pygtex) [190]
(./_minted-Tutorial/9457A436D281E066D350873A88476E599D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5C1399E579A6AA8D432E509AE441C2AE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7528F52197E46B376DB12FB34672D7A8EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/64ACD8E8EC2C5F323A9D84639080EBCB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C8BC3187BF8F96BDF009A2CA8A95A3C39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4323DBBD15E176599A70095217F377E79D788471CB66B7D26E11C71E228
489B2.pygtex [191])
(./_minted-Tutorial/0B895A7CD7770AD5152A902E24E861699D788471CB66B7D26E11C71E228
489B2.pygtex)) [192] (./Tutorial/chapter_pdb.tex
Chapter 11.

(./_minted-Tutorial/D779A8F555F6BCC207B905D5D6C228539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/946CAECCFDBF1349958F40A0FC03463F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2FDED7F9BEF9EA1F5CE28B11996ED43D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/05714E0F28AC6B36B176161D8A9FA84D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3D3953EF520FE9546FC19DB705E690859D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E37E6F74461E0075B61AF24790D37C719D788471CB66B7D26E11C71E228
489B2.pygtex [193])
(./_minted-Tutorial/32D78458130807D5C8DD536942BA73889D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B49437C8CCF1C8D72B8DBA0CFE1DCB359D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A7F199DA98E2BD66B92177EFD14AA59A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/57A82B690A435E6AD7DAD62778DB82319D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3AABC2CB1B50E66D5DBACF20EF52245A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C79D210A6D0E5501910FFF311063879E9D788471CB66B7D26E11C71E228
489B2.pygtex) [194]
(./_minted-Tutorial/41FC845107E552AB47AA881B90236E189D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B41B5BFD7D85ED4E7E70DA059AE1D1769D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36AD36AC9E663BF06BB871053927CDF09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1BBCC7F8F1756C270C4D99E9F943A0249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4AD3361A8DEC1848967C5C4904CBAA6B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8411ECFB826F8858D5702457B0FB9A59D788471CB66B7D26E11C71E228
489B2.pygtex) [195]
(./_minted-Tutorial/684AC0ECE33D6BA84F0409CE669AB1369D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C85B5FA2C9BF8127C2FEFF62553FECEC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/05AAA27695D5E74A2F0C892230E4EFA49D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.022pt too wide) in paragraph at lines 262--264
\OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m
/n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/Model/Chain/Residue/Ato
m)
[196] Excluding 'htmlonly' comment.
(./_minted-Tutorial/DCB043864D9F8E2B59DEBF1784B30CDC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B6B956752D54554859CB3FC041890BD79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/958010CCD8250B2A6D359F037738B54E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/69627B7F3108FCBC466F45AE8D24D9799D788471CB66B7D26E11C71E228
489B2.pygtex) [197] [198 <./images/smcra.png (PNG copy)>]
(./_minted-Tutorial/13774A78311C8B2B99285E3D509AD8559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EC253507D414D1E9DDE9BC5CAF6BC78C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/69D3F9059506073A988980B78CEAB2479D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5A42A68287048A843E1066F2E27276229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22421A9A4B194CFEBFABE1E2DDFC8A129D788471CB66B7D26E11C71E228
489B2.pygtex) [199]
(./_minted-Tutorial/8A579A2F82E38AFC725C7AD02B2F5D579D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C4346C691565244D87DFA5ED26B512E39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/38F92E91F7EF83579513DC2A23D231DC9D788471CB66B7D26E11C71E228
489B2.pygtex) [200]
(./_minted-Tutorial/35E34E333445AAAA4E33570211335BA59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A2470AECC1DA459F7A1ACC68FCD911B19D788471CB66B7D26E11C71E228
489B2.pygtex [201])
(./_minted-Tutorial/874F41EC8F1C0D727A004EAEFDC880989D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/94A9BE470837AFDA4B8581B79BB124929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/76657140082404C594EE786B642215C39D788471CB66B7D26E11C71E228
489B2.pygtex [202])
(./_minted-Tutorial/17EB0A1D2812B68E199CC00449B9254C9D788471CB66B7D26E11C71E228
489B2.pygtex) [203]
(./_minted-Tutorial/D94A742238FBA8E89BB46038CDBDEB909D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BFD7EDA2178705DA7C24F4D3735823E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/73DA0F97AF01C85175F4AF2DFAE2C6B79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7E80E6D2D75417229F3B2B705315B1289D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/618AFB68C3893C2A344D3A532D9BD99A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/82DD3285068398C1A65910EDE1BE970C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0799FD26AFF50D33D257B86E8D3E40B39D788471CB66B7D26E11C71E228
489B2.pygtex [204])
(./_minted-Tutorial/2857EE83D7FCEE22018F0C0AD63239E09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/365D7E5A27BEEE6ED9265079DF2318999D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B35B80BBDE5AE1373CAE9105C01A6249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BDCD0910528B95EADEE1C7C6BD40AD3C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3A499902396CBA88B311EE3A93BC26639D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B2412D9441598FCD30172739CB3CCA399D788471CB66B7D26E11C71E228
489B2.pygtex [205])
(./_minted-Tutorial/728242DAC9077785511462C5CD16E6679D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/866FA21894DE0E73CE09F7F50E59FDC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D6328A6D8E47F7B8E9530D396E8ED50D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2CF9B1EBC15ECA1536AFA86FAF01899B9D788471CB66B7D26E11C71E228
489B2.pygtex [206])
(./_minted-Tutorial/F412BF266412BEC93BB127CA53AB4D0C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A73938953B2223965D08B528F27C56E89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B33389074760A02AC27316E67DAAB0739D788471CB66B7D26E11C71E228
489B2.pygtex [207])
Overfull \hbox (42.26714pt too wide) in paragraph at lines 956--960
\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 976--996
[][] 
[208]
(./_minted-Tutorial/10F60558792DABA08CE906FCD09A993C9D788471CB66B7D26E11C71E228
489B2.pygtex)

LaTeX Warning: Command \r invalid in math mode on input line 1049.


(./_minted-Tutorial/10BEDFA26FE20B8B11FC832131C1705E9D788471CB66B7D26E11C71E228
489B2.pygtex) [209]
(./_minted-Tutorial/12DBC9D94FB0B4B78A481C6C111C67099D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/895E3343902EFB0E5475667B01C4B6919D788471CB66B7D26E11C71E228
489B2.pygtex) [210] [211]
(./_minted-Tutorial/7A6D5A10ECC42BAFEE724455549BCB159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D5B0F5228C1E7FAD0C7AB40AEFF6B6A99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2810A7579DC6FE011D31E2F074471A749D788471CB66B7D26E11C71E228
489B2.pygtex [212])
(./_minted-Tutorial/D9D0B8746EBF14CF4BE7DA480D9ECD5D9D788471CB66B7D26E11C71E228
489B2.pygtex) [213]) [214] (./Tutorial/chapter_popgen.tex
Chapter 12.

(./_minted-Tutorial/E5F1866C3CBB485B8C06B62764ACFBB2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/331BEE386F268F55DE217F54E27EAB6BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [215]
(./_minted-Tutorial/6CD64A1F591B16F512F7EB6B68E5B3FCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)) [216] (./Tutorial/chapter_phylo.tex
Chapter 13.

(./_minted-Tutorial/8F8EFC1C83277AE6C5B5A259FAAC5671EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/4914B4679D1C933D9AD76E95F18CE15841CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/3D758844BE2A5D4414B741470EDE8C249D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/719B0C758B666CDEEB2B250C2143A4AD9D788471CB66B7D26E11C71E228
489B2.pygtex [217])
(./_minted-Tutorial/8698B66B622D8A91E7706D889D5F35DD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6621A01BB423374C8FC608E267D0EA7D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B99D788471CB66B7D26E11C71E228
489B2.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/6C5156DAD460519324A5B7657B301B5D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1836031BC83AA94C8906762F613E6CBA9D788471CB66B7D26E11C71E228
489B2.pygtex) [218]
(./_minted-Tutorial/D0A75FB8C1C791E4AA80420B93F216A89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FEC6C2CB5FA0AFCFE00D995BD3642FF29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2B435DC3041611A5D6A663B437ADB1AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (25.13162pt too wide) in paragraph at lines 182--185
[]\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t
he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor

(./_minted-Tutorial/29624A9666C9430AABADF395148BBF279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D0F05D42BA0A9BC594EEDB16319A972D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/87517FEF82BFE1AB8D89A83F4DC5E8B99D788471CB66B7D26E11C71E228
489B2.pygtex [219 <./images/phylo-simple-draw.png>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/D713148814BA75DCDEB1C77B12674D9B9D788471CB66B7D26E11C71E228
489B2.pygtex [220 <./images/phylo-color-draw.png>])
(./_minted-Tutorial/69333D76AA5D97D8BF9E95DEECEEE2B19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/456F5679DCD4FF740E7A110889D865739D788471CB66B7D26E11C71E228
489B2.pygtex [221])
(./_minted-Tutorial/2B3BFA62F3A778E4818959ED3E8AD3EE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/08F738B2988883F2B3BAD96FA439AD7C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8C7F4AB58CCB44E2FF66E36A26E59F559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/00BD91C09868B2B26E32B5FB41A2583C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A1E441205EAE188E6F4319753E3982D39D788471CB66B7D26E11C71E228
489B2.pygtex [222])
(./_minted-Tutorial/C3E382424C6F17EF8DB95D08D8AC9FEE9D788471CB66B7D26E11C71E228
489B2.pygtex) Excluding 'htmlonly' comment. [223 <./images/phylo-draw-example.p
ng>]
Overfull \hbox (19.85507pt too wide) in paragraph at lines 479--486
\OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, 
[][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"})
[224]
Overfull \hbox (13.48741pt too wide) in paragraph at lines 534--537
[]\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, 
find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10
 ,
[225]
(./_minted-Tutorial/6AAB725DBD2E5B7C5FD79A9A16536BF6D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [226]
Overfull \hbox (15.04868pt too wide) in paragraph at lines 703--707
[]\OT1/cmr/m/n/10 Below is an ex-am-ple on how to use a python script to in-ter
-act with PhyML ([][]$\OT1/cmtt/m/n/10 http : / / www . atgc-[]montpellier .

(./_minted-Tutorial/20AACD5E58630D4B64529F3A1ACD81199D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EB4CA3626331FD00CE50FECC3590095B9D788471CB66B7D26E11C71E228
489B2.pygtex) [227]
(./_minted-Tutorial/0702C9875263768417DD3ED2EF78755E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C395044A3DB827E8D2E36BA5259475D29D788471CB66B7D26E11C71E228
489B2.pygtex) [228]) [229] (./Tutorial/chapter_motifs.tex
Chapter 14.

(./_minted-Tutorial/9344D5588F066D22473BF4F77E39E1F39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AB934E1AD357BE20BA1F223A29AE486A9D788471CB66B7D26E11C71E228
489B2.pygtex [230])
(./_minted-Tutorial/A7AAAF382950D3CAD77D17E6B6489D039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CEBDE9089C5A4F125D8DD8D4E6ACD9C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9293BA115F68336B4D0213D24C96AE759D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/BFC042DE8B1588B2D23A8510A608989C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5F3B74C4B4D1FF3D387E6F57F726D1779D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0517D975CF92331B81AF837F9D2571739D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C66E35936EA68A132264FDF63F70A42A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/86717C2BCE65F41FCDB86527631658579D788471CB66B7D26E11C71E228
489B2.pygtex [231])
(./_minted-Tutorial/8572965E772BA3D97A5ACAB64A3CEA2B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0CFCBF886B5144440F79F612431920229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/02A6CF1EA94D619AE2B9428BDA4531C59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EDCE72CAE83814FFFF4AE6A97CBB24769D788471CB66B7D26E11C71E228
489B2.pygtex) [232]
(./_minted-Tutorial/C6095CA0913B3D01D81200EBA18DE7FAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex [233])
(./_minted-Tutorial/2CAEA4D1EDEE84068D05546A212DB0C69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD1D7AEBB145784C9665DAA472D55CE29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/30EDED7029501226C973943BBA0D1ECD9D788471CB66B7D26E11C71E228
489B2.pygtex [234])
(./_minted-Tutorial/5C8E141CD14F7220B986B96A3E564D14EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/95F985CC0D974FEE28E0B2667232BA3F9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E778DA34B5EC9B33527CC22435275C769D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D11003572C5456D15CB1BF6CD74B860E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD308858A86E4C77FD58BD7CFCB2EF92EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [235])
(./_minted-Tutorial/4910FFD3FDCDF743F7F37BE10B04F7069D788471CB66B7D26E11C71E228
489B2.pygtex [236])
(./_minted-Tutorial/AF4CF0FDC0B4EBF46401E9953A293EF59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7D8B23E400A55050254232F7CA2CC9E19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0E771A916EB510C91DEEBFC8201442DC9D788471CB66B7D26E11C71E228
489B2.pygtex [237])
(./_minted-Tutorial/1C14559B3C7AC9C35B84F1518D8088FD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/46FF514D13E6C4030C26EC4EFF8CFAFD9D788471CB66B7D26E11C71E228
489B2.pygtex [238])
(./_minted-Tutorial/8E9A5519710E4288CC6DA45EFD61B3AE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/47B231A79951117DFE8D7B369F5A0EDE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CF5314A9EF9BBFFA32CFF87ADC53C3789D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD7EDF217AC860547FAAC456716F6D6B9D788471CB66B7D26E11C71E228
489B2.pygtex [239])
(./_minted-Tutorial/7EC0366BAB057E95DD30855AF8AD06F8EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/805B769BEA8271618919879EBC73D6ABEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/AD271A766709EB68A386A406C3E3DCB0EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/3C12150A1943B695BB045865F0A87E44EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [240])
(./_minted-Tutorial/95318595464A829C3F1A431E3C76909F9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.10551pt too wide) in paragraph at lines 603--606
\OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man
d reads the com-plete file di-rectly, so you can close the file af-ter call-ing
 [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 .

(./_minted-Tutorial/147DE2DA7F37C2A5A1C1344033AB8B849D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/36E981BB5EF7EC3A1829EC830B0AF9C29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/22F78F0EFBBBF61FA3DB5795B5820CD79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F87F681AD46E2F9ABF3B87ADA8B1EFB69D788471CB66B7D26E11C71E228
489B2.pygtex [241])
(./_minted-Tutorial/CB1A766DCCC9D440884673396E0120539D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/64B1E8E30714DF156170A704E0AF9B9EEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/744EE283B3B7A72BE718EF244D782CA7EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [242])
(./_minted-Tutorial/BCCDFDD968CCC98039C6D6F4886917C19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/2F48F226FED2AEC7A54EAA6C769060B99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9D8413811B6BC75226431D501B682BD99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4293959D98D2DC2DC0CE6CA72DFD5D5C9D788471CB66B7D26E11C71E228
489B2.pygtex)

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

[243]
(./_minted-Tutorial/86BE687BF0F504548CFBA35246A755EF9D788471CB66B7D26E11C71E228
489B2.pygtex [244])
(./_minted-Tutorial/21510EFF9B5DA96F8CCEE8DFB8F264069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B5EBBADDB3E7B53C5C4AED82E42FFC49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0B25C484239457B0395121E60BF514959D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F8B39433E243DA74D8945D4CCEE706059D788471CB66B7D26E11C71E228
489B2.pygtex [245])
(./_minted-Tutorial/46C8C36973CB3D67D276A48C8EA6FEE09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/99B6E6DD45FE4AED26044A4FD1A68C749D788471CB66B7D26E11C71E228
489B2.pygtex [246])
(./_minted-Tutorial/001DF21D4EE824968A1A6CCAE41948EB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5CBFAEFFA194A41048B5DAFCF4C988129D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E2EC88874CB26E442AD8A92E3073E2259D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/176227E746894D602FF7231BCB8E5F219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B9A36F2FAD2C11328984E7BBD1033E489D788471CB66B7D26E11C71E228
489B2.pygtex [247])
(./_minted-Tutorial/31F98B5F648636905472A89ADB4396EA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6E38B20582EF8FBF09C0864F13C6172D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D36079E59E9C6C6FCEFB62B1C38D03DC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/949879BACF1AC9FDD5E01F1FDF5D0C7B9D788471CB66B7D26E11C71E228
489B2.pygtex [248])
(./_minted-Tutorial/CEF4EF7AD2559AA1A840E9E5F4F1E33E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8A4D3A313CCE21054A332F39A60F4F8D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8AC6389F07C07315B68A4843F8EC4A819D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CD7B5AA933F3E10D95D901D3BB5DA1619D788471CB66B7D26E11C71E228
489B2.pygtex) [249]
(./_minted-Tutorial/21D3336F2855CBE535339D390FE18E259D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/33B5E369AD9661A05C861A5AE12A50929D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A80C26CD370CE20C0095D5E8948B4CA29D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/34B3515117C70C6DAC332384F14FD0D09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/6EC91D6C707FE27D0D4D730403C860739D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B3D49921528F0B11F6E5813C6062BEC59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3712C0CA690A1E7FF72D1693AABFE9709D788471CB66B7D26E11C71E228
489B2.pygtex [250])
(./_minted-Tutorial/4F50929124655BC08B3D6057B14984E59D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DA79BC51C090F498913A417759345DF49D788471CB66B7D26E11C71E228
489B2.pygtex [251])
(./_minted-Tutorial/4B2423E325126B67BF464F894752E3229D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/25136DD7F6E2BE72E81866FB3F2A41C99D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/50111CA97C115B1826E19F91E69CE8BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9E8A7295F5BEF290E7F4283BD72616039D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D5F089B3901176BD3F7658EA70DA24739D788471CB66B7D26E11C71E228
489B2.pygtex [252])
(./_minted-Tutorial/753220AB94A0DA3FD9F8379D30465A7A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/35B38D8BFFB75E06C84D419CF8CBB21B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A6DBEC036FAC23CE4697722B836743C19D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DF57AC6C176D67E4A7B147371D11BA169D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B593C755A27EDDCAF56E94C0930898D39D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/53BF343E6B63B739979E29182E1485D39D788471CB66B7D26E11C71E228
489B2.pygtex) [253]
(./_minted-Tutorial/868ABF9ABD2736A12F423306646D77069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/912C817861E626118AB2FA06F12910B69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/62D830B5536F542C80973708E7B78A269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4A6B49E72A96FB6AC93E0E280B4F4472EF9ECD8502EC2CF3722B913689E
0BC32.pygtex) [254]
(./_minted-Tutorial/F99AB908B88D7B819F597C02D259A52B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/CB4926B7151E97486270449C8F84AB419D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/852A3852541269829CE5DF380357F2CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AC8B7A8ADEC6FEB0B1260E665CF238B69D788471CB66B7D26E11C71E228
489B2.pygtex) [255]) [256] (./Tutorial/chapter_cluster.tex
Chapter 15.
[257] [258] [259] [260]
(./_minted-Tutorial/C7B59059E3AE6CDE790EFE6EB0ED41409D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C2B72A7408C7DF74DFCEBE04859972879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/425EDAA643B5AA9589F3EEE6017358279D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/50B5971EFCF22FCC4E1302DB2D0A2500D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/293084E63EA5C0E01F325A4DD59469C09D788471CB66B7D26E11C71E228
489B2.pygtex [261])
Overfull \hbox (78.60634pt too wide) in paragraph at lines 245--246
\OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra
nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$

(./_minted-Tutorial/05DC01C08B8EDF71F86E3C3A9C28EB349D788471CB66B7D26E11C71E228
489B2.pygtex) [262] [263]
(./_minted-Tutorial/A4A28B5A443208DEAB3B4D76AA3B762E9D788471CB66B7D26E11C71E228
489B2.pygtex) [264]
(./_minted-Tutorial/C286E2777B917B774560CBDC7CF926269D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED18D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7ACD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [265] [266]
Overfull \hbox (16.73593pt too wide) in paragraph at lines 423--424
[][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them.
 The items be-ing clus-tered are num-bered from 0 to $[]$,

(./_minted-Tutorial/015798D317E9D8732518AFD186C997CA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A27E6BF4EEB8E8B1C2390492678617399D788471CB66B7D26E11C71E228
489B2.pygtex) [267]
(./_minted-Tutorial/81E4060E427D22B8F0C63B69EEC10A2A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B8D2A546EC4941692F427A363193FBDE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A54EF6455421EFDFA1F63EB361CD74F69D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8975A4CCBC4C6138C302117E04F203AD9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/636486BB1CF700F6391685224211BE229D788471CB66B7D26E11C71E228
489B2.pygtex) [268]
(./_minted-Tutorial/6EFE1AC811BF16FF597EBE3E25BD2F729D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/F8E41E59FD44DADEB3740B0C0ED17D419D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/1B924FC8FA13A8B73C1C9E6EF88950559D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/77B32E49165B4345FFCA9FACF597BEEB9D788471CB66B7D26E11C71E228
489B2.pygtex [269])
(./_minted-Tutorial/D04E097D8E8C4C039FEC20FA103CED18D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/36EF8931044EF448BC70F722AFADB43DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/805B33438269C932AC54C0DAB5A3D7ACD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [270]
(./_minted-Tutorial/E542C07D0131DF56A89D92F80416C1759D788471CB66B7D26E11C71E228
489B2.pygtex) [271]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 654--656
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/7476A2D5F9D3A46EE00108837901FAEA9D788471CB66B7D26E11C71E228
489B2.pygtex) [272]
(./_minted-Tutorial/0420D397BA03971C0079F52E55FEABAB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8D3928D79091BFFA7AFB6D6F35A52C7C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4D59CC328F454A26A4BE9F91740D961C9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (25.39864pt too wide) in paragraph at lines 739--750
 [] 
[273] [274]
(./_minted-Tutorial/EFB8602799AD543446B386107A8147F79D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/43B30B527C3A2D8148F25CA143719CAF9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/C77F1ABB31C6A53C1626E0E0B34BB0FC9D788471CB66B7D26E11C71E228
489B2.pygtex) [275]
(./_minted-Tutorial/1F3E2EFB988F2639C701A920B547241D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/3CAD921471DA4CA4441D02558CD1F2E09D788471CB66B7D26E11C71E228
489B2.pygtex [276])
(./_minted-Tutorial/1A863BDE3A5754AA2C865F2A82DA85049D788471CB66B7D26E11C71E228
489B2.pygtex) [277]
Overfull \hbox (106.77225pt too wide) in paragraph at lines 929--931
\OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered,
 or $[]$

(./_minted-Tutorial/A39469F362670EDC6C7E8FD9FDF412C49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/12B5F20EFF78F0E8FE505D45A9786D709D788471CB66B7D26E11C71E228
489B2.pygtex [278])
(./_minted-Tutorial/E6C8D570402CFDDB43A6AE5A198BCF589D788471CB66B7D26E11C71E228
489B2.pygtex))
Overfull \hbox (26.21434pt too wide) in paragraph at lines 986--116
[]\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result
_K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT
1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 
. 
[279] (./Tutorial/chapter_learning.tex
Chapter 16.
[280]
(./_minted-Tutorial/A66CDD6792A98054D498A97A3A920D4D9D788471CB66B7D26E11C71E228
489B2.pygtex [281])
(./_minted-Tutorial/390D9013E6AF7385E3C5A71EC44014AA9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/9153ABDB5D850EC42F344B9B42C10E4F9D788471CB66B7D26E11C71E228
489B2.pygtex [282])
(./_minted-Tutorial/183EBB0903E699FF7289E5FDA71CB0969D788471CB66B7D26E11C71E228
489B2.pygtex [283])
(./_minted-Tutorial/7E494FD25838EE4C9E476EBA48BDF0CE9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B53BAB1CC7569CE8ADFECF2CFC02D4029D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0201F5A7D34B6F74CAF2C8723DA28C0A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/906DB90E50544D69A8A7FA2703E3A0129D788471CB66B7D26E11C71E228
489B2.pygtex [284])

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


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


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


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


(./_minted-Tutorial/AE2B91C0366D79644B870EB1EB9436E69D788471CB66B7D26E11C71E228
489B2.pygtex) [285]

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


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


(./_minted-Tutorial/B35CDBE12860937BD1F854583E7BA5959D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B38BF6A3D910590D450B331A075B723C9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/E59729DAB9242AE915A0943E44B8DF9B9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/AEF267C3082CB68394DCEE656CEB2FC19D788471CB66B7D26E11C71E228
489B2.pygtex [286])
(./_minted-Tutorial/A38355D92EE3DC8D96655428C0CEDC159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A586FFDD9483C890754DBE5DFC4207109D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/8F9899A476407D923F0AEB91D4FF3D359D788471CB66B7D26E11C71E228
489B2.pygtex [287])) [288] (./Tutorial/chapter_graphics.tex
Chapter 17.
[289]
(./_minted-Tutorial/775A7C8BD2C1E8942CA7A717928F51A0D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/997BE59EDA00B2D427337713C8A7E3D9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/684A3C9C1713469B78289C6B9952D816D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F1FF3DF6D6F3CDAA260F74B59EE3502FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/864F43F6883D29AB2276A3D7B4C4B035D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/F52EB727435E5F7D4D3C22DD13755CA7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [290]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/68BE5A2D2503535D27E3B265B36AB36ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [291 <./images/plasmid_linear.png (PNG copy)>]) [292 <./images/pla
smid_circular.png (PNG copy)>]
(./_minted-Tutorial/ECF4549C3ED9BED5D89616D96689FF27D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F6FC21242AEF7E7CBB38249DA932A735D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/E9061B00D3D1F94D19518B622458CA8BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/869D4007B198B35A03870134DB69E5F2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/83AFE18710C133D7AFEBCF65D9D3D850D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [293]) Excluding 'htmlonly' comment.
(./_minted-Tutorial/7767B7CE8DD842D17DB77A8BF9691B94D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/B7F9EB41E9BA682D9273C414D13CA80CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [294] [295 <./images/GD_sigil_labels.png (PNG copy)>])
Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
(./_minted-Tutorial/6EE3865BBB66BBD15ABFD7BAE73F8FEBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/74C150D1D11511477A4CD9DC0CD7863AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/2216BF82E557F1E99146777612D2BA8FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/67B3F646AA5F8690151428081229D39BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [296] [297 <./images/GD_sigils.png>] [298 <./images/GD_sigil_arrow
_shafts.png>] [299 <./images/GD_sigil_arrow_heads.png>] [300])
Excluding 'htmlonly' comment. [301 <./images/plasmid_linear_nice.png (PNG copy)
>] [302 <./images/plasmid_circular_nice.png>]
(./_minted-Tutorial/7CAF22FEDE98A6B9B7990010CA8709DCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/FA676816242752C9FE9F5EB12D4DAA89D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [303])
(./_minted-Tutorial/7926619D7609A591C404A01B2A99177AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [304]) Excluding 'htmlonly' comment. [305 <./images/three_track_si
mple.png>]
(./_minted-Tutorial/A2465D4E8908256A31684D5DDE7DA111D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/347EB36A3001532221DDF6C29AA04AFBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [306])
(./_minted-Tutorial/F46F39DD7A8EC7B20CD42ACF6EFD1840D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/2CF2D2FC7E96B3F426F22452724A4C28D5CCE6351B83FE352E9906AED2A
3B7C6.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. [307] Excluding 'htmlonly' comment. [308 <./image
s/three_track_cl.png>] [309 <./images/three_track_cl2a.png>]
(./_minted-Tutorial/F9FFB9659EC22BC166AEB6F728414977D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/A9695DE54C455E13B400269BF9F424FED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F545B5C3D394029AA34E76D27DC2DBAFD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/3BACFFDF9009929D690C44BF09EFB67FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [310]
(./_minted-Tutorial/0AC11BF466D4AA0B0536F05378BEC9CCD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/F5380F7F462C2A51219D9EF8994C192CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [311] [312 <./images/simple_chrom.pdf> <./images/tRNA_chrom.pdf>])
Excluding 'htmlonly' comment.
(./_minted-Tutorial/7B75AD289117B9F25E36C48BBFCB0A75D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [313]) Excluding 'htmlonly' comment.) [314]
(./Tutorial/chapter_kegg.tex
Chapter 18.

(./_minted-Tutorial/27731B46F813E809C1F5AB60C050CD4A9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4FAF7CA55B5CBF29D4D0569020062C719D788471CB66B7D26E11C71E228
489B2.pygtex) [315]
(./_minted-Tutorial/39B217C0E81B95398ED4BBC9D1B0F5CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D9724C7E513E9BF6FDCCF6A64359AD4BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [316])
(./_minted-Tutorial/64868CEDE925B08BA4840E27792F9C95EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)) [317] (./Tutorial/chapter_phenotype.tex
Chapter 19.

(./_minted-Tutorial/252224E77AA1520CEA1F05EB2C082F8D9D788471CB66B7D26E11C71E228
489B2.pygtex) [318]
(./_minted-Tutorial/1742F69ECDDF3F5D15E6B5DBFEFA97219D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/4835A2D15014EC539B36FCA111ABBB449D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FD6100DF6B4884776EB70DBE176DB0819D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/943877B8F1F5B9C773FB1AA7B24E159E9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/0BDF372B652AEF5EA570E28DA8244BF89D788471CB66B7D26E11C71E228
489B2.pygtex [319])
(./_minted-Tutorial/BE8D8FA0E8D3D6C871BF41D7B5DEB51D9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/290D0631491AEE7E10A3CE09C85D72069D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EA2967473FD2864501AEB5123E3D579D9D788471CB66B7D26E11C71E228
489B2.pygtex [320])
(./_minted-Tutorial/AEDB3BBBBA5C2503EDA86617E08721889D788471CB66B7D26E11C71E228
489B2.pygtex [321])
(./_minted-Tutorial/43A346E75A27D33FDB3F346C240E06E69D788471CB66B7D26E11C71E228
489B2.pygtex)) [322] (./Tutorial/chapter_cookbook.tex
Chapter 20.

(./_minted-Tutorial/D080533227BF139CB7F7C56D06E7D6EBD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [323])
(./_minted-Tutorial/CA0835D76EF6887731674D8AB555091BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1F5CA35662EA2CAC7BDBA9D33CDB13A09D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/A3BD1DBCF883DB2E1DD394B912E571649D788471CB66B7D26E11C71E228
489B2.pygtex) [324]
(./_minted-Tutorial/C6B2C783E94EA95E84DF3F108F727AD49D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/EC0DF654B46A2F2CE5F2C795E0321ED2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/19A3D00CDA3CDDA100F55F41BCAAF54FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [325])
(./_minted-Tutorial/FF8E30AFA718C8DC6288D5C9AD354F64D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/019E169CFF67EC7D891D6A0239647061D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/9CFE18F499906D88CC2737F15500C03BD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [326])
(./_minted-Tutorial/C2311B95BFB64D51B766D16ACEF028DDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D6A48411D1CBD21E55ABF85BFBC65541D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7448CA91BF0AA6E19C1517B6DE408793D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [327]
(./_minted-Tutorial/C3FBD2FC664129F7A578076AD05E79D9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/38576C78990D3D95691E2AC6EB80ABA2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [328]
(./_minted-Tutorial/D08928CA73DF435476A35E8ADF641831D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/D51441AC892832CAA5031DFFA5F35450D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
Overfull \hbox (5.83499pt too wide) in paragraph at lines 454--458
\OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul
d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator

(./_minted-Tutorial/AB16E58608A2F17CC79E692955720887D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [329])
Overfull \hbox (4.57849pt too wide) in paragraph at lines 475--477
\OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849.
fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[
]primer.fastq\OT1/cmr/m/n/10 . 

(./_minted-Tutorial/6D336A88208F39729D1A90FF60CB5EBDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/2C62FFE33ECD45881AC7A8296BCCA556D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7E077104A49653CA66AAC778C604E64AD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [330])
(./_minted-Tutorial/ECD311074B098CDA38E7451A88AC0F9CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [331]
(./_minted-Tutorial/CC6E723850600015A2C6BAC6C88F8915D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [332]
(./_minted-Tutorial/1E88A30624397E1FA5202CD67F078C31D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/55F15E0B4613AC1B2AC177DC40737367D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/C6B1FCFF3C4616196F6CE060D97D25879D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/7B877C459BB3438E40CD76B614F605B6D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [333])
(./_minted-Tutorial/C47681A25A04F989A9657602F996D5B5D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/20E6EE0734FD2ED211933BE632478CABD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/BF6F632251CC051592D2BE57B36A38A0D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/C8587EE0D03D0937B88179912FC3582E9D788471CB66B7D26E11C71E228
489B2.pygtex [334])
(./_minted-Tutorial/7F8C2BBB4F26A8E6A0FD7BCC41E2BB809D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/FCE533CC3550AB6D1B3C6F6ED53E0CEB9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/37A86DCC1F181ADAA1855D9EBC303BAC41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/474B445E26A3CD55A1BA5820E4D03C7D9D788471CB66B7D26E11C71E228
489B2.pygtex [335])
(./_minted-Tutorial/DDBEEE137CB936CA422E560A63FB97B89D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/B802763B27D7694A759DB2EBF16EF0989D788471CB66B7D26E11C71E228
489B2.pygtex) [336]
(./_minted-Tutorial/EE9671DEE2B114F544A5881F074C33B2D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/5A7FB5AC8923F9582CAE20A770A63052EF9ECD8502EC2CF3722B913689E
0BC32.pygtex [337])
(./_minted-Tutorial/8F229FE70B397EEE7D48ECD1D5BAD1CC9D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/71434DB3B51372DFED40CEB6F06647B7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [338]) Excluding 'htmlonly' comment.
Overfull \hbox (4.00363pt too wide) in paragraph at lines 1117--1120
[]\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10
 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use
 [][]\OT1/cmtt/m/n/10 pylab.savefig(...)

(./_minted-Tutorial/798776F436EA559BACD9C305C0997391D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [339 <./images/hist_plot.png>])
(./_minted-Tutorial/CB78AD94DFE82ADBAF348C0EC1D261CDD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment. Excluding 'htmlonly' comment.
[340 <./images/gc_plot.png>]
(./_minted-Tutorial/6E0DA723E11A7B9CA8E2353A984B5DF7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/80A47C8780CE3021D53829563E816656D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [341 <./images/dot_plot.png>])
(./_minted-Tutorial/9574E55C4A182E2A0201DF18689F52F4D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/24C65C38DAD936B7AA15C7ED02EA36B3D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/6655B5CD97C33186A22E6897501301FFD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [342])
(./_minted-Tutorial/7727E7020AA1BDC4C2A426B7590C20ADD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment. [343 <./images/dot_plot_scatter.png
>]
(./_minted-Tutorial/601CCA4B782F1DA528DB81B024803195D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) Excluding 'htmlonly' comment.
(./_minted-Tutorial/9D2779E6D02C00C016A7A73A452EBC73D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [344]
(./_minted-Tutorial/06CAA397021B5D0CD904B7CF0209DCA3D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [345 <./images/SRR001666.png>]
(./_minted-Tutorial/16711B0A63F93BBACAF3C86CFFB7BEFAEF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/96EC77291C119EF69670ACDB1C35CE21EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/6C14F4F0692168BA7165351C706B643DD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E686FC2D122CF1560FAF4512CD53777FD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E09A8EBF1B7CB9F831FC2D9DA4814535D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/E598995EF885D7803642E8685DCB8F90EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
Overfull \hbox (49.0755pt too wide) in paragraph at lines 1528--1529
[]\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l
ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c
mr/m/n/10 .

(./_minted-Tutorial/7F027F6FD8E839F99A1077399D9B8EFF9D788471CB66B7D26E11C71E228
489B2.pygtex [346])
(./_minted-Tutorial/25AF2FA7C23EEF982CD3578DCB530065D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/7662755469082A25B2A4B53656D96A40D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/EA8748814B0C57E7E4D7F8619D00D043D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [347])
(./_minted-Tutorial/99476F758194110AC0ED8AAAFD8ECB7CD5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/504DC4F75F719CFF95C5294B2961C9739D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/486C8450148EF1EADB63A41AB9A896FA9D788471CB66B7D26E11C71E228
489B2.pygtex [348])
(./_minted-Tutorial/DD48495FAB2341AA078121E9286C07179D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/DE31628D815724B7B422A1012BAA0C379D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/5740381D1C5E453AC66BA80B494079159D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/19B054992CCA481AA19D78F9C6DD93BF9D788471CB66B7D26E11C71E228
489B2.pygtex)
Overfull \hbox (13.15053pt too wide) in paragraph at lines 1703--1704
\OT1/cmr/m/n/10 two [][]\OT1/cmtt/m/n/10 residue_frequencies []\OT1/cmr/m/n/10 
val-ues mul-ti-plied with each other. For ex-am-ple, [][]\OT1/cmtt/m/n/10 expec
ted_frequencies[^^MD^^M, ^^ME^^M]

(./_minted-Tutorial/40ECF2E139F38209730D3B02B624EF749D788471CB66B7D26E11C71E228
489B2.pygtex [349])
(./_minted-Tutorial/8965C8E87A0A43ECCE216C12F7DE7A4F9D788471CB66B7D26E11C71E228
489B2.pygtex)) [350] (./Tutorial/chapter_testing.tex
Chapter 21.

(./_minted-Tutorial/867AD481B37AFD4F1A17FC0F2F42FCAE41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/E8078015A2C53794A733DDC875BD062141CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/754EBE4BCCE307413E74F18728530D0441CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/E40D6903CCE8EA230C75C80B7C2D907341CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/BC243371043473AEE20C23FF0FABFF0D41CFBAB8D39E8FFAF3C5D885168
6F649.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
[351]
(./_minted-Tutorial/9373056942403CCACDB96B0F438E4B64EF9ECD8502EC2CF3722B913689E
0BC32.pygtex)
(./_minted-Tutorial/2A1F0B8D037B993D748BF652420448ED41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex [352])
(./_minted-Tutorial/61465735FDB5BC7ADF12D7A4628FC9A7D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex) [353]
(./_minted-Tutorial/826F7B9143F73D7CFCAB00906377DAB9D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/B1E279D3993E4775FBE4555B6DD342AD41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/313C740A73E814DA220EB71149FE706ED5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [354])
(./_minted-Tutorial/99DA0A53F2BD41D9D1BCE2B0332444F441CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/4916E014295B56C6CDDB3C287542DA29D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/1B0AB11BDA71CF4763A5A4A8B8297711D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [355])
(./_minted-Tutorial/7A0DBB9735CDAA1699A6FA164701062F41CFBAB8D39E8FFAF3C5D885168
6F649.pygtex) [356]
(./_minted-Tutorial/3E57444149EF1ACC12DA2995F5B0345641CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/DD3A1A642CB850F292FC934F9336EC4341CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)) [357] (./Tutorial/chapter_contributing.tex
Chapter 22.
[358]
(./_minted-Tutorial/7713FA97EA16E9508BA3E6B94494492541CFBAB8D39E8FFAF3C5D885168
6F649.pygtex)
(./_minted-Tutorial/61D19A91BF1A1F95030292E40EF87A3641CFBAB8D39E8FFAF3C5D885168
6F649.pygtex) [359]) [360] (./Tutorial/chapter_appendix.tex
Chapter 23.

(./_minted-Tutorial/109DA6882E9B770A79B0E47E5D014D329D788471CB66B7D26E11C71E228
489B2.pygtex)
(./_minted-Tutorial/D8DF7F2BE4A1010E81F7C5AD3A462859D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/268983882DD871BC94F164D025D08B42D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex [361])
(./_minted-Tutorial/940D9D0165FD2273E52C2D203CE26C42D5CCE6351B83FE352E9906AED2A
3B7C6.pygtex)
(./_minted-Tutorial/4B521F4803AD1FD3B86D09A2ECD5A2039D788471CB66B7D26E11C71E228
489B2.pygtex)) [362] [363] [364] [365] (./Tutorial.aux
(./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux)
(./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux)
(./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux)
(./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux)
(./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux)
(./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux)
(./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux)
(./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux)
(./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux)
(./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux)
(./Tutorial/chapter_testing.aux) (./Tutorial/chapter_contributing.aux)
(./Tutorial/chapter_appendix.aux))

LaTeX Warning: There were undefined references.


LaTeX Warning: There were multiply-defined labels.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb
xti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmitt10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmr5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on Tutorial.pdf (366 pages, 2519617 bytes).
Transcript written on Tutorial.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2022-11-01>
L3 programming layer <2022-11-02>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2022/07/02 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.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/txtbabel.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf))
(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file biopdb_faq.aux.
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: a4paper
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: 
* h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt)
* v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt)
* \paperwidth=597.50787pt
* \paperheight=845.04684pt
* \textwidth=418.25368pt
* \textheight=731.23584pt
* \oddsidemargin=17.3571pt
* \evensidemargin=17.3571pt
* \topmargin=-52.36449pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=10.0pt
* \footskip=30.0pt
* \marginparwidth=65.0pt
* \marginparsep=11.0pt
* \columnsep=10.0pt
* \skip\footins=9.0pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidefalse
* \@mparswitchfalse
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

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

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

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

[4] [5]

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

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

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


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


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

[9]

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


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

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

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

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

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

LaTeX Warning: There were undefined references.


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


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

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/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, 163401 bytes).
Transcript written on biopdb_faq.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2022-11-01>
L3 programming layer <2022-11-02>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2022/07/02 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.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/txtbabel.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf))
(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./biopdb_faq.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: a4paper
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: 
* h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt)
* v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt)
* \paperwidth=597.50787pt
* \paperheight=845.04684pt
* \textwidth=418.25368pt
* \textheight=731.23584pt
* \oddsidemargin=17.3571pt
* \evensidemargin=17.3571pt
* \topmargin=-52.36449pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=10.0pt
* \footskip=30.0pt
* \marginparwidth=65.0pt
* \marginparsep=11.0pt
* \columnsep=10.0pt
* \skip\footins=9.0pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidefalse
* \@mparswitchfalse
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

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

Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318
\T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to
 a list of ref-er-ences), \T1/pcr/m/n/10 journal_-
[4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10]
Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016
\T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co
n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 .

Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024
\T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob-
tained from the \T1/pcr/m/n/10 Polypeptide
[11] [12]
Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149
[]\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e
xposure(model)  

Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174
\T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1
/pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m
/n/10 get_vector
[13] [14]
Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353
[]\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE 
DIS-CLAIM
[15] (./biopdb_faq.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/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, 165319 bytes).
Transcript written on biopdb_faq.log.
pdflatex biopdb_faq.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./biopdb_faq.tex
LaTeX2e <2022-11-01>
L3 programming layer <2022-11-02>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2022/07/02 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/bookman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.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/txtbabel.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf))
(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./biopdb_faq.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: a4paper
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: 
* h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt)
* v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt)
* \paperwidth=597.50787pt
* \paperheight=845.04684pt
* \textwidth=418.25368pt
* \textheight=731.23584pt
* \oddsidemargin=17.3571pt
* \evensidemargin=17.3571pt
* \topmargin=-52.36449pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=10.0pt
* \footskip=30.0pt
* \marginparwidth=65.0pt
* \marginparsep=11.0pt
* \columnsep=10.0pt
* \skip\footins=9.0pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidefalse
* \@mparswitchfalse
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

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

Overfull \hbox (11.71707pt too wide) in paragraph at lines 312--318
\T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to
 a list of ref-er-ences), \T1/pcr/m/n/10 journal_-
[4] [5] [6] [7 <./images/smcra.png (PNG copy)>] [8] [9] [10]
Overfull \hbox (45.08351pt too wide) in paragraph at lines 1012--1016
\T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co
n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 .

Overfull \hbox (10.80998pt too wide) in paragraph at lines 1020--1024
\T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob-
tained from the \T1/pcr/m/n/10 Polypeptide
[11] [12]
Overfull \hbox (87.74638pt too wide) in paragraph at lines 1148--1149
[]\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e
xposure(model)  

Overfull \hbox (20.6135pt too wide) in paragraph at lines 1169--1174
\T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1
/pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m
/n/10 get_vector
[13] [14]
Overfull \hbox (1.21811pt too wide) in paragraph at lines 1345--1353
[]\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE 
DIS-CLAIM
[15] (./biopdb_faq.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/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, 165319 bytes).
Transcript written on biopdb_faq.log.
make[2]: Leaving directory '/<<BUILDDIR>>/python-biopython-1.80+dfsg/Doc'
make[1]: Leaving directory '/<<BUILDDIR>>/python-biopython-1.80+dfsg'
	rm -f debian/python3-biopython.debhelper.log
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-biopython-1.80+dfsg'
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 "3.11 3.10" --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:240: set -e; \
                             mkdir -p /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/home; \
                             mkdir -p /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Doc/examples; \
                             cp -a Doc/Tutorial.tex /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Doc/Tutorial /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Doc/examples /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Tests /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build; \
                             cd /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests; \
                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/home python3.11 run_tests.py --offline
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests/run_tests.py:33: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  import distutils.util
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils.
  warnings.warn(
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
test_Ace ... ok
test_Affy ... ok
test_AlignIO ... ok
test_AlignIO_ClustalIO ... ok
test_AlignIO_EmbossIO ... ok
test_AlignIO_FastaIO ... ok
test_AlignIO_MauveIO ... ok
test_AlignIO_PhylipIO ... ok
test_AlignIO_convert ... ok
test_AlignInfo ... ok
test_Align_Alignment ... ok
test_Align_a2m ... ok
test_Align_bed ... ok
test_Align_bigbed ... ok
test_Align_bigmaf ... ok
test_Align_bigpsl ... ok
test_Align_clustal ... ok
test_Align_emboss ... ok
test_Align_exonerate ... ok
test_Align_fasta ... ok
test_Align_hhr ... ok
test_Align_maf ... ok
test_Align_mauve ... ok
test_Align_msf ... ok
test_Align_nexus ... ok
test_Align_phylip ... ok
test_Align_psl ... ok
test_Align_sam ... ok
test_Align_stockholm ... ok
test_Align_tabular ... ok
test_Application ... ok
test_BWA_tool ... ok
test_BioSQL_MySQLdb_online ... skipping. internet not available
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
test_BioSQL_mysql_connector_online ... skipping. internet not available
test_BioSQL_psycopg2_online ... skipping. internet not available
test_BioSQL_sqlite3 ... ok
test_BioSQL_sqlite3_online ... skipping. internet not available
test_Blast_Record ... ok
test_CAPS ... ok
test_Chi2 ... ok
test_ClustalOmega_tool ... ok
test_Clustalw_tool ... ok
test_Cluster ... ok
test_CodonTable ... ok
test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics.

test_Compass ... ok
test_Consensus ... ok
test_Dialign_tool ... ok
test_EMBL_unittest ... ok
test_Emboss ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_EmbossPrimer ... ok
test_Entrez ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Entrez/__init__.py:686: UserWarning: 
            Email address is not specified.

            To make use of NCBI's E-utilities, NCBI requires you to specify your
            email address with each request.  As an example, if your email address
            is A.N.Other@example.com, you can specify it as follows:
               from Bio import Entrez
               Entrez.email = 'A.N.Other@example.com'
            In case of excessive usage of the E-utilities, NCBI will attempt to contact
            a user at the email address provided before blocking access to the
            E-utilities.
  warnings.warn(
ok
test_Entrez_online ... skipping. internet not available
test_Entrez_parser ... ok
test_Enzyme ... ok
test_ExPASy ... skipping. internet not available
test_Fasttree_tool ... ok
test_File ... ok
test_GenBank ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics.

test_GraphicsBitmaps ... skipping. Error: Install ReportLab's renderPM module if you want to create bitmaps with Bio.Graphics.

test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics.

test_GraphicsDistribution ... loading tests failed:
Failed to import test module: test_GraphicsDistribution
Traceback (most recent call last):
  File "/usr/lib/python3.11/unittest/loader.py", line 154, in loadTestsFromName
    module = __import__(module_name)
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests/test_GraphicsDistribution.py", line 28, in <module>
    from Bio.Graphics.Distribution import BarChartDistribution
  File "/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/Distribution.py", line 22, in <module>
    from reportlab.lib import colors
  File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in <module>
    from reportlab.lib.rl_accel import fp_str
  File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in <module>
    from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes
  File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in <module>
    from PIL import Image
  File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in <module>
    from . import _imaging as core
ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)

test_GraphicsGeneral ... loading tests failed:
Failed to import test module: test_GraphicsGeneral
Traceback (most recent call last):
  File "/usr/lib/python3.11/unittest/loader.py", line 154, in loadTestsFromName
    module = __import__(module_name)
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests/test_GraphicsGeneral.py", line 25, in <module>
    from Bio.Graphics.Comparative import ComparativeScatterPlot
  File "/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Graphics/Comparative.py", line 14, in <module>
    from reportlab.lib import colors
  File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in <module>
    from reportlab.lib.rl_accel import fp_str
  File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in <module>
    from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes
  File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in <module>
    from PIL import Image
  File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in <module>
    from . import _imaging as core
ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)

test_HMMCasino ... ok
test_HMMGeneral ... ok
test_KEGG ... ok
test_KEGG_online ... skipping. internet not available
test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics.
test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics.
test_KGML_nographics ... ok
test_KeyWList ... ok
test_LogisticRegression ... ok
test_MafIO_index ... ok
test_Mafft_tool ... ok
test_MarkovModel ... ok
test_Medline ... ok
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
test_NCBITextParser ... ok
test_NCBIXML ... ok
test_NCBI_BLAST_tools ... ok
test_NCBI_qblast ... ok
test_NMR ... ok
test_NaiveBayes ... ok
test_Nexus ... ok
test_PAML_baseml ... ok
test_PAML_codeml ... ok
test_PAML_yn00 ... ok
test_PDBList ... skipping. internet not available
test_PDB_CEAligner ... ok
test_PDB_DSSP ... ok
test_PDB_Dice ... ok
test_PDB_Disordered ... ok
test_PDB_Exposure ... ok
test_PDB_FragmentMapper ... ok
test_PDB_KDTree ... ok
test_PDB_MMCIF2Dict ... ok
test_PDB_MMCIFIO ... ok
test_PDB_MMCIFParser ... ok
test_PDB_NACCESS ... ok
test_PDB_PDBIO ... ok
test_PDB_PDBParser ... ok
test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
test_PDB_Polypeptide ... ok
test_PDB_QCSuperimposer ... ok
test_PDB_SASA ... ok
test_PDB_SMCRA ... ok
test_PDB_Selection ... ok
test_PDB_StructureAlignment ... ok
test_PDB_Superimposer ... ok
test_PDB_internal_coords ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/PDB/Polypeptide.py:161: BiopythonDeprecationWarning: 'one_to_three' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_1to3'.
  warnings.warn(
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 ... skipping. Install matplotlib if you want to use Bio.Phylo._utils.
test_Phylo_networkx ... ok
test_PopGen_GenePop_nodepend ... ok
test_Prank_tool ... ok
test_Probcons_tool ... ok
test_ProtParam ... ok
test_RCSBFormats ... ok
test_Restriction ... ok
test_SCOP_Astral ... ok
test_SCOP_Cla ... ok
test_SCOP_Des ... ok
test_SCOP_Dom ... ok
test_SCOP_Hie ... ok
test_SCOP_Raf ... ok
test_SCOP_Residues ... ok
test_SCOP_Scop ... ok
test_SCOP_online ... skipping. internet not available
test_SVDSuperimposer ... ok
test_SearchIO_blast_tab ... ok
test_SearchIO_blast_tab_index ... ok
test_SearchIO_blast_text ... ok
test_SearchIO_blast_xml ... ok
test_SearchIO_blast_xml_index ... ok
test_SearchIO_blat_psl ... ok
test_SearchIO_blat_psl_index ... ok
test_SearchIO_exonerate ... ok
test_SearchIO_exonerate_text_index ... ok
test_SearchIO_exonerate_vulgar_index ... ok
test_SearchIO_fasta_m10 ... ok
test_SearchIO_fasta_m10_index ... ok
test_SearchIO_hhsuite2_text ... ok
test_SearchIO_hmmer2_text ... ok
test_SearchIO_hmmer2_text_index ... ok
test_SearchIO_hmmer3_domtab ... ok
test_SearchIO_hmmer3_domtab_index ... ok
test_SearchIO_hmmer3_tab ... ok
test_SearchIO_hmmer3_tab_index ... ok
test_SearchIO_hmmer3_text ... ok
test_SearchIO_hmmer3_text_index ... ok
test_SearchIO_interproscan_xml ... ok
test_SearchIO_legacy ... ok
test_SearchIO_model ... ok
test_SearchIO_write ... ok
test_SeqFeature ... ok
test_SeqIO ... ok
test_SeqIO_AbiIO ... ok
test_SeqIO_FastaIO ... ok
test_SeqIO_Gck ... ok
test_SeqIO_Insdc ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_SeqIO_NibIO ... ok
test_SeqIO_PdbIO ... ok
test_SeqIO_QualityIO ... ok
test_SeqIO_SeqXML ... ok
test_SeqIO_SnapGene ... ok
test_SeqIO_TwoBitIO ... ok
test_SeqIO_Xdna ... ok
test_SeqIO_features ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:550: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
  warnings.warn(
ok
test_SeqIO_index ... ok
test_SeqIO_online ... skipping. internet not available
test_SeqIO_write ... ok
test_SeqRecord ... ok
test_SeqUtils ... ok
test_Seq_objs ... ok
test_SffIO ... ok
test_SwissProt ... ok
test_TCoffee_tool ... ok
test_TogoWS ... skipping. internet not available
test_TreeConstruction ... ok
test_Tutorial ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(
ok
test_UniGene ... ok
test_UniProt_GOA ... ok
test_Uniprot ... ok
test_Wise ... ok
test_align ... ok
test_align_substitution_matrices ... ok
test_bgzf ... ok
test_cellosaurus ... ok
test_codonalign ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython.
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/Seq.py:3457: 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(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA)
  warnings.warn(
ok
test_geo ... ok
test_kNN ... ok
test_motifs ... ok
test_motifs_online ... skipping. internet not available
test_pairwise2 ... ok
test_pairwise2_no_C ... ok
test_pairwise_aligner ... ok
test_pairwise_alignment_map ... ok
test_phenotype ... ok
test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality.
test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
test_prodoc ... ok
test_prosite ... ok
test_samtools_tool ... ok
test_seq ... ok
test_translate ... ok
Bio docstring test ... ok
Bio.Affy docstring test ... ok
Bio.Affy.CelFile docstring test ... ok
Bio.Align docstring test ... ok
Bio.Align.AlignInfo docstring test ... ok
Bio.Align.Applications docstring test ... ok
Bio.Align.Applications._ClustalOmega docstring test ... ok
Bio.Align.Applications._Clustalw docstring test ... ok
Bio.Align.Applications._Dialign docstring test ... ok
Bio.Align.Applications._MSAProbs docstring test ... ok
Bio.Align.Applications._Mafft docstring test ... ok
Bio.Align.Applications._Muscle docstring test ... ok
Bio.Align.Applications._Prank docstring test ... ok
Bio.Align.Applications._Probcons docstring test ... ok
Bio.Align.Applications._TCoffee docstring test ... ok
Bio.Align._aligners docstring test ... ok
Bio.Align.a2m docstring test ... ok
Bio.Align.bed docstring test ... ok
Bio.Align.bigbed docstring test ... ok
Bio.Align.bigmaf docstring test ... ok
Bio.Align.bigpsl docstring test ... ok
Bio.Align.clustal docstring test ... ok
Bio.Align.emboss docstring test ... ok
Bio.Align.exonerate docstring test ... ok
Bio.Align.fasta docstring test ... ok
Bio.Align.hhr docstring test ... ok
Bio.Align.interfaces docstring test ... ok
Bio.Align.maf docstring test ... ok
Bio.Align.mauve docstring test ... ok
Bio.Align.msf docstring test ... ok
Bio.Align.nexus docstring test ... ok
Bio.Align.phylip docstring test ... ok
Bio.Align.psl docstring test ... ok
Bio.Align.sam docstring test ... ok
Bio.Align.stockholm docstring test ... ok
Bio.Align.substitution_matrices docstring test ... ok
Bio.Align.tabular docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.ClustalIO docstring test ... ok
Bio.AlignIO.EmbossIO docstring test ... ok
Bio.AlignIO.FastaIO docstring test ... ok
Bio.AlignIO.Interfaces docstring test ... ok
Bio.AlignIO.MafIO docstring test ... ok
Bio.AlignIO.MauveIO docstring test ... ok
Bio.AlignIO.MsfIO docstring test ... ok
Bio.AlignIO.NexusIO docstring test ... ok
Bio.AlignIO.PhylipIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Application docstring test ... ok
Bio.Blast docstring test ... ok
Bio.Blast.Applications docstring test ... ok
Bio.Blast.NCBIWWW docstring test ... ok
Bio.Blast.NCBIXML docstring test ... ok
Bio.Blast.ParseBlastTable docstring test ... ok
Bio.Blast.Record docstring test ... ok
Bio.CAPS docstring test ... ok
Bio.Cluster docstring test ... ok
Bio.Cluster._cluster docstring test ... ok
Bio.Compass docstring test ... ok
Bio.Data docstring test ... ok
Bio.Data.CodonTable docstring test ... ok
Bio.Data.IUPACData docstring test ... ok
Bio.Data.PDBData docstring test ... ok
Bio.Data.SCOPData docstring test ... ok
Bio.Emboss docstring test ... ok
Bio.Emboss.Applications docstring test ... ok
Bio.Emboss.Primer3 docstring test ... ok
Bio.Emboss.PrimerSearch docstring test ... ok
Bio.Entrez.Parser docstring test ... ok
Bio.ExPASy.Enzyme docstring test ... ok
Bio.ExPASy.Prodoc docstring test ... ok
Bio.ExPASy.Prosite docstring test ... ok
Bio.ExPASy.ScanProsite docstring test ... ok
Bio.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 ... FAIL, ImportError
Bio.Graphics.ColorSpiral docstring test ... ok
Bio.Graphics.Comparative docstring test ... FAIL, ImportError
Bio.Graphics.DisplayRepresentation docstring test ... FAIL, ImportError
Bio.Graphics.Distribution docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._AbstractDrawer docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._CircularDrawer docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._Colors docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._CrossLink docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._Diagram docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._Feature docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._FeatureSet docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._Graph docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._GraphSet docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._LinearDrawer docstring test ... FAIL, ImportError
Bio.Graphics.GenomeDiagram._Track docstring test ... FAIL, ImportError
Bio.Graphics.KGML_vis docstring test ... skipped, missing Python dependency
Bio.HMM docstring test ... ok
Bio.HMM.DynamicProgramming docstring test ... ok
Bio.HMM.MarkovModel docstring test ... ok
Bio.HMM.Trainer docstring test ... ok
Bio.HMM.Utilities docstring test ... ok
Bio.KEGG docstring test ... ok
Bio.KEGG.Compound docstring test ... ok
Bio.KEGG.Enzyme docstring test ... ok
Bio.KEGG.Gene docstring test ... ok
Bio.KEGG.KGML docstring test ... ok
Bio.KEGG.KGML.KGML_parser docstring test ... ok
Bio.KEGG.KGML.KGML_pathway docstring test ... ok
Bio.KEGG.Map docstring test ... ok
Bio.KEGG.REST docstring test ... ok
Bio.LogisticRegression docstring test ... ok
Bio.MarkovModel docstring test ... ok
Bio.MaxEntropy docstring test ... ok
Bio.Medline docstring test ... ok
Bio.NMR docstring test ... ok
Bio.NMR.NOEtools docstring test ... ok
Bio.NMR.xpktools docstring test ... ok
Bio.NaiveBayes docstring test ... ok
Bio.Nexus docstring test ... ok
Bio.Nexus.Nexus docstring test ... ok
Bio.Nexus.Nodes docstring test ... ok
Bio.Nexus.StandardData docstring test ... ok
Bio.Nexus.Trees docstring test ... ok
Bio.Nexus.cnexus docstring test ... ok
Bio.PDB docstring test ... ok
Bio.PDB.AbstractPropertyMap docstring test ... ok
Bio.PDB.Atom docstring test ... ok
Bio.PDB.Chain docstring test ... ok
Bio.PDB.DSSP docstring test ... ok
Bio.PDB.Dice docstring test ... ok
Bio.PDB.Entity docstring test ... ok
Bio.PDB.FragmentMapper docstring test ... ok
Bio.PDB.HSExposure docstring test ... ok
Bio.PDB.MMCIF2Dict docstring test ... ok
Bio.PDB.MMCIFParser docstring test ... ok
Bio.PDB.Model docstring test ... ok
Bio.PDB.NACCESS docstring test ... ok
Bio.PDB.NeighborSearch docstring test ... ok
Bio.PDB.PDBExceptions docstring test ... ok
Bio.PDB.PDBIO docstring test ... ok
Bio.PDB.PDBList docstring test ... ok
Bio.PDB.PDBParser docstring test ... ok
Bio.PDB.PICIO docstring test ... ok
Bio.PDB.PSEA docstring test ... ok
Bio.PDB.Polypeptide docstring test ... ok
Bio.PDB.QCPSuperimposer docstring test ... ok
Bio.PDB.QCPSuperimposer.qcprotmodule docstring test ... ok
Bio.PDB.Residue docstring test ... ok
Bio.PDB.ResidueDepth docstring test ... ok
Bio.PDB.SASA docstring test ... ok
Bio.PDB.SCADIO docstring test ... ok
Bio.PDB.Selection docstring test ... ok
Bio.PDB.Structure docstring test ... ok
Bio.PDB.StructureAlignment docstring test ... ok
Bio.PDB.StructureBuilder docstring test ... ok
Bio.PDB.Superimposer docstring test ... ok
Bio.PDB.ccealign docstring test ... ok
Bio.PDB.cealign docstring test ... ok
Bio.PDB.ic_data docstring test ... ok
Bio.PDB.ic_rebuild docstring test ... ok
Bio.PDB.internal_coords docstring test ... ok
Bio.PDB.kdtrees docstring test ... ok
Bio.PDB.mmcifio docstring test ... ok
Bio.PDB.mmtf docstring test ... ok
Bio.PDB.mmtf.DefaultParser docstring test ... ok
Bio.PDB.mmtf.mmtfio docstring test ... ok
Bio.PDB.parse_pdb_header docstring test ... ok
Bio.PDB.qcprot docstring test ... ok
Bio.PDB.vectors docstring test ... ok
Bio.Pathway docstring test ... ok
Bio.Pathway.Rep docstring test ... ok
Bio.Pathway.Rep.Graph docstring test ... ok
Bio.Pathway.Rep.MultiGraph docstring test ... ok
Bio.Phylo docstring test ... ok
Bio.Phylo.Applications docstring test ... ok
Bio.Phylo.Applications._Fasttree docstring test ... ok
Bio.Phylo.Applications._Phyml docstring test ... ok
Bio.Phylo.Applications._Raxml docstring test ... ok
Bio.Phylo.BaseTree docstring test ... ok
Bio.Phylo.CDAO docstring test ... ok
Bio.Phylo.CDAOIO docstring test ... ok
Bio.Phylo.Consensus docstring test ... ok
Bio.Phylo.NeXML docstring test ... ok
Bio.Phylo.NeXMLIO docstring test ... ok
Bio.Phylo.Newick docstring test ... ok
Bio.Phylo.NewickIO docstring test ... ok
Bio.Phylo.NexusIO docstring test ... ok
Bio.Phylo.PAML docstring test ... ok
Bio.Phylo.PAML._paml docstring test ... ok
Bio.Phylo.PAML._parse_baseml docstring test ... ok
Bio.Phylo.PAML._parse_codeml docstring test ... ok
Bio.Phylo.PAML._parse_yn00 docstring test ... ok
Bio.Phylo.PAML.baseml docstring test ... ok
Bio.Phylo.PAML.chi2 docstring test ... ok
Bio.Phylo.PAML.codeml docstring test ... ok
Bio.Phylo.PAML.yn00 docstring test ... ok
Bio.Phylo.PhyloXML docstring test ... ok
Bio.Phylo.PhyloXMLIO docstring test ... ok
Bio.Phylo.TreeConstruction docstring test ... ok
Bio.Phylo._cdao_owl docstring test ... ok
Bio.Phylo._io docstring test ... ok
Bio.Phylo._utils docstring test ... ok
Bio.PopGen docstring test ... ok
Bio.PopGen.GenePop docstring test ... ok
Bio.PopGen.GenePop.Controller docstring test ... ok
Bio.PopGen.GenePop.EasyController docstring test ... ok
Bio.PopGen.GenePop.FileParser docstring test ... ok
Bio.PopGen.GenePop.LargeFileParser docstring test ... ok
Bio.Restriction docstring test ... ok
Bio.Restriction.PrintFormat docstring test ... ok
Bio.Restriction.Restriction docstring test ... ok
Bio.Restriction.Restriction_Dictionary docstring test ... ok
Bio.SCOP docstring test ... ok
Bio.SCOP.Cla docstring test ... ok
Bio.SCOP.Des docstring test ... ok
Bio.SCOP.Dom docstring test ... ok
Bio.SCOP.Hie docstring test ... ok
Bio.SCOP.Raf docstring test ... ok
Bio.SCOP.Residues docstring test ... ok
Bio.SVDSuperimposer docstring test ... ok
Bio.SearchIO docstring test ... ok
Bio.SearchIO.BlastIO docstring test ... ok
Bio.SearchIO.BlastIO.blast_tab docstring test ... ok
Bio.SearchIO.BlastIO.blast_text docstring test ... ok
Bio.SearchIO.BlastIO.blast_xml docstring test ... ok
Bio.SearchIO.BlatIO docstring test ... ok
Bio.SearchIO.ExonerateIO docstring test ... ok
Bio.SearchIO.ExonerateIO._base docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... ok
Bio.SearchIO.FastaIO docstring test ... ok
Bio.SearchIO.HHsuiteIO docstring test ... ok
Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... ok
Bio.SearchIO.HmmerIO docstring test ... ok
Bio.SearchIO.HmmerIO._base docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... ok
Bio.SearchIO.InterproscanIO docstring test ... ok
Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... ok
Bio.SearchIO._index docstring test ... ok
Bio.SearchIO._legacy docstring test ... ok
Bio.SearchIO._legacy.NCBIStandalone docstring test ... ok
Bio.SearchIO._legacy.ParserSupport docstring test ... ok
Bio.SearchIO._model docstring test ... ok
Bio.SearchIO._model._base docstring test ... ok
Bio.SearchIO._model.hit docstring test ... ok
Bio.SearchIO._model.hsp docstring test ... ok
Bio.SearchIO._model.query docstring test ... ok
Bio.SearchIO._utils docstring test ... ok
Bio.Seq docstring test ... ok
Bio.SeqFeature docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.AbiIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqIO.FastaIO docstring test ... ok
Bio.SeqIO.GckIO docstring test ... ok
Bio.SeqIO.IgIO docstring test ... ok
Bio.SeqIO.InsdcIO docstring test ... ok
Bio.SeqIO.Interfaces docstring test ... ok
Bio.SeqIO.NibIO docstring test ... ok
Bio.SeqIO.PdbIO docstring test ... ok
Bio.SeqIO.PhdIO docstring test ... ok
Bio.SeqIO.PirIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.SeqXmlIO docstring test ... ok
Bio.SeqIO.SffIO docstring test ... ok
Bio.SeqIO.SnapGeneIO docstring test ... ok
Bio.SeqIO.SwissIO docstring test ... ok
Bio.SeqIO.TabIO docstring test ... ok
Bio.SeqIO.TwoBitIO docstring test ... ok
Bio.SeqIO.UniprotIO docstring test ... ok
Bio.SeqIO.XdnaIO docstring test ... ok
Bio.SeqIO._index docstring test ... ok
Bio.SeqIO._twoBitIO docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.SeqUtils.CheckSum docstring test ... ok
Bio.SeqUtils.CodonUsage docstring test ... ok
Bio.SeqUtils.CodonUsageIndices docstring test ... ok
Bio.SeqUtils.IsoelectricPoint docstring test ... ok
Bio.SeqUtils.MeltingTemp docstring test ... ok
Bio.SeqUtils.ProtParam docstring test ... ok
Bio.SeqUtils.ProtParamData docstring test ... ok
Bio.SeqUtils.lcc docstring test ... ok
Bio.Sequencing docstring test ... ok
Bio.Sequencing.Ace docstring test ... ok
Bio.Sequencing.Applications docstring test ... ok
Bio.Sequencing.Applications._Novoalign docstring test ... ok
Bio.Sequencing.Applications._bwa docstring test ... ok
Bio.Sequencing.Applications._samtools docstring test ... ok
Bio.Sequencing.Phd docstring test ... ok
Bio.SwissProt docstring test ... ok
Bio.SwissProt.KeyWList docstring test ... ok
Bio.UniGene docstring test ... ok
Bio.UniProt docstring test ... ok
Bio.UniProt.GOA docstring test ... ok
Bio.Wise docstring test ... ok
Bio.Wise.dnal docstring test ... ok
Bio.Wise.psw docstring test ... ok
Bio._utils docstring test ... ok
Bio.bgzf docstring test ... ok
Bio.codonalign docstring test ... ok
Bio.codonalign.codonalignment docstring test ... ok
Bio.codonalign.codonseq docstring test ... ok
Bio.cpairwise2 docstring test ... ok
Bio.kNN docstring test ... ok
Bio.motifs docstring test ... ok
Bio.motifs._pwm docstring test ... ok
Bio.motifs.alignace docstring test ... ok
Bio.motifs.applications docstring test ... ok
Bio.motifs.applications._xxmotif docstring test ... ok
Bio.motifs.clusterbuster docstring test ... ok
Bio.motifs.jaspar docstring test ... ok
Bio.motifs.jaspar.db docstring test ... skipped, missing Python dependency
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 ... skipped, missing Python dependency
BioSQL docstring test ... ok
BioSQL.BioSeq docstring test ... ok
BioSQL.BioSeqDatabase docstring test ... ok
BioSQL.DBUtils docstring test ... ok
BioSQL.Loader docstring test ... ok
ERROR while importing Bio.Graphics.BasicChromosome: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.Comparative: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.DisplayRepresentation: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.Distribution: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._AbstractDrawer: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._CircularDrawer: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._Colors: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._CrossLink: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._Diagram: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._Feature: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._FeatureSet: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._Graph: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._GraphSet: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._LinearDrawer: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
ERROR while importing Bio.Graphics.GenomeDiagram._Track: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
----------------------------------------------------------------------
Ran 553 tests in 857.831 seconds

FAILED (failures = 18)
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec  7 2022, 08:49:13) [GCC 12.2.0]
Operating system: posix linux
E: pybuild pybuild:379: test: plugin custom failed with: exit code=1: set -e; \
                             mkdir -p /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/home; \
                             mkdir -p /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Doc/examples; \
                             cp -a Doc/Tutorial.tex /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Doc/Tutorial /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Doc/examples /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Doc; \
                             cp -a Tests /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build; \
                             cd /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests; \
                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/home python3.11 run_tests.py --offline
I: pybuild base:240: set -e; \
                             mkdir -p /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/home; \
                             mkdir -p /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Doc/examples; \
                             cp -a Doc/Tutorial.tex /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Doc; \
                             cp -a Doc/Tutorial /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Doc; \
                             cp -a Doc/examples /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Doc; \
                             cp -a Tests /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build; \
                             cd /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Tests; \
                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/home python3.10 run_tests.py --offline
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Tests/run_tests.py:33: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  import distutils.util
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils.
  warnings.warn(
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
test_Ace ... ok
test_Affy ... ok
test_AlignIO ... ok
test_AlignIO_ClustalIO ... ok
test_AlignIO_EmbossIO ... ok
test_AlignIO_FastaIO ... ok
test_AlignIO_MauveIO ... ok
test_AlignIO_PhylipIO ... ok
test_AlignIO_convert ... ok
test_AlignInfo ... ok
test_Align_Alignment ... ok
test_Align_a2m ... ok
test_Align_bed ... ok
test_Align_bigbed ... ok
test_Align_bigmaf ... ok
test_Align_bigpsl ... ok
test_Align_clustal ... ok
test_Align_emboss ... ok
test_Align_exonerate ... ok
test_Align_fasta ... ok
test_Align_hhr ... ok
test_Align_maf ... ok
test_Align_mauve ... ok
test_Align_msf ... ok
test_Align_nexus ... ok
test_Align_phylip ... ok
test_Align_psl ... ok
test_Align_sam ... ok
test_Align_stockholm ... ok
test_Align_tabular ... ok
test_Application ... ok
test_BWA_tool ... ok
test_BioSQL_MySQLdb_online ... skipping. internet not available
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
test_BioSQL_mysql_connector_online ... skipping. internet not available
test_BioSQL_psycopg2_online ... skipping. internet not available
test_BioSQL_sqlite3 ... ok
test_BioSQL_sqlite3_online ... skipping. internet not available
test_Blast_Record ... ok
test_CAPS ... ok
test_Chi2 ... ok
test_ClustalOmega_tool ... ok
test_Clustalw_tool ... ok
test_Cluster ... ok
test_CodonTable ... ok
test_ColorSpiral ... ok
test_Compass ... ok
test_Consensus ... ok
test_Dialign_tool ... ok
test_EMBL_unittest ... ok
test_Emboss ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_EmbossPrimer ... ok
test_Entrez ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Entrez/__init__.py:686: UserWarning: 
            Email address is not specified.

            To make use of NCBI's E-utilities, NCBI requires you to specify your
            email address with each request.  As an example, if your email address
            is A.N.Other@example.com, you can specify it as follows:
               from Bio import Entrez
               Entrez.email = 'A.N.Other@example.com'
            In case of excessive usage of the E-utilities, NCBI will attempt to contact
            a user at the email address provided before blocking access to the
            E-utilities.
  warnings.warn(
ok
test_Entrez_online ... skipping. internet not available
test_Entrez_parser ... ok
test_Enzyme ... ok
test_ExPASy ... skipping. internet not available
test_Fasttree_tool ... ok
test_File ... ok
test_GenBank ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_GenomeDiagram ... Warn: Can't find .pfb for face 'Times-Roman'
ok
test_GraphicsBitmaps ... skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics
Error in setFont('Times-Roman',10) 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 ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
test_NCBITextParser ... ok
test_NCBIXML ... ok
test_NCBI_BLAST_tools ... ok
test_NCBI_qblast ... ok
test_NMR ... ok
test_NaiveBayes ... ok
test_Nexus ... ok
test_PAML_baseml ... ok
test_PAML_codeml ... ok
test_PAML_yn00 ... ok
test_PDBList ... skipping. internet not available
test_PDB_CEAligner ... ok
test_PDB_DSSP ... ok
test_PDB_Dice ... ok
test_PDB_Disordered ... ok
test_PDB_Exposure ... ok
test_PDB_FragmentMapper ... ok
test_PDB_KDTree ... ok
test_PDB_MMCIF2Dict ... ok
test_PDB_MMCIFIO ... ok
test_PDB_MMCIFParser ... ok
test_PDB_NACCESS ... ok
test_PDB_PDBIO ... ok
test_PDB_PDBParser ... ok
test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
test_PDB_Polypeptide ... ok
test_PDB_QCSuperimposer ... ok
test_PDB_SASA ... ok
test_PDB_SMCRA ... ok
test_PDB_Selection ... ok
test_PDB_StructureAlignment ... ok
test_PDB_Superimposer ... ok
test_PDB_internal_coords ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/PDB/Polypeptide.py:161: BiopythonDeprecationWarning: 'one_to_three' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_1to3'.
  warnings.warn(
ok
test_PDB_parse_pdb_header ... ok
test_PDB_vectors ... ok
test_PQR ... ok
test_Pathway ... ok
test_Phd ... ok
test_Phylo ... ok
test_PhyloXML ... ok
test_Phylo_CDAO ... ok
test_Phylo_NeXML ... ok
test_Phylo_matplotlib ... ok
test_Phylo_networkx ... ok
test_PopGen_GenePop_nodepend ... ok
test_Prank_tool ... ok
test_Probcons_tool ... ok
test_ProtParam ... ok
test_RCSBFormats ... ok
test_Restriction ... ok
test_SCOP_Astral ... ok
test_SCOP_Cla ... ok
test_SCOP_Des ... ok
test_SCOP_Dom ... ok
test_SCOP_Hie ... ok
test_SCOP_Raf ... ok
test_SCOP_Residues ... ok
test_SCOP_Scop ... ok
test_SCOP_online ... skipping. internet not available
test_SVDSuperimposer ... ok
test_SearchIO_blast_tab ... ok
test_SearchIO_blast_tab_index ... ok
test_SearchIO_blast_text ... ok
test_SearchIO_blast_xml ... ok
test_SearchIO_blast_xml_index ... ok
test_SearchIO_blat_psl ... ok
test_SearchIO_blat_psl_index ... ok
test_SearchIO_exonerate ... ok
test_SearchIO_exonerate_text_index ... ok
test_SearchIO_exonerate_vulgar_index ... ok
test_SearchIO_fasta_m10 ... ok
test_SearchIO_fasta_m10_index ... ok
test_SearchIO_hhsuite2_text ... ok
test_SearchIO_hmmer2_text ... ok
test_SearchIO_hmmer2_text_index ... ok
test_SearchIO_hmmer3_domtab ... ok
test_SearchIO_hmmer3_domtab_index ... ok
test_SearchIO_hmmer3_tab ... ok
test_SearchIO_hmmer3_tab_index ... ok
test_SearchIO_hmmer3_text ... ok
test_SearchIO_hmmer3_text_index ... ok
test_SearchIO_interproscan_xml ... ok
test_SearchIO_legacy ... ok
test_SearchIO_model ... ok
test_SearchIO_write ... ok
test_SeqFeature ... ok
test_SeqIO ... ok
test_SeqIO_AbiIO ... ok
test_SeqIO_FastaIO ... ok
test_SeqIO_Gck ... ok
test_SeqIO_Insdc ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_SeqIO_NibIO ... ok
test_SeqIO_PdbIO ... ok
test_SeqIO_QualityIO ... ok
test_SeqIO_SeqXML ... ok
test_SeqIO_SnapGene ... ok
test_SeqIO_TwoBitIO ... ok
test_SeqIO_Xdna ... ok
test_SeqIO_features ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:550: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
  warnings.warn(
ok
test_SeqIO_index ... ok
test_SeqIO_online ... skipping. internet not available
test_SeqIO_write ... ok
test_SeqRecord ... ok
test_SeqUtils ... ok
test_Seq_objs ... ok
test_SffIO ... ok
test_SwissProt ... ok
test_TCoffee_tool ... ok
test_TogoWS ... skipping. internet not available
test_TreeConstruction ... ok
test_Tutorial ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(
ok
test_UniGene ... ok
test_UniProt_GOA ... ok
test_Uniprot ... ok
test_Wise ... ok
test_align ... ok
test_align_substitution_matrices ... ok
test_bgzf ... ok
test_cellosaurus ... ok
test_codonalign ... /<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/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(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/Seq.py:3457: 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(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
  warnings.warn(
/<<BUILDDIR>>/python-biopython-1.80+dfsg/.pybuild/cpython3_3.10/build/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA)
  warnings.warn(
ok
test_geo ... ok
test_kNN ... ok
test_motifs ... ok
test_motifs_online ... skipping. internet not available
test_pairwise2 ... ok
test_pairwise2_no_C ... ok
test_pairwise_aligner ... ok
test_pairwise_alignment_map ... ok
test_phenotype ... ok
test_phenotype_fit ... ok
test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
test_prodoc ... ok
test_prosite ... ok
test_samtools_tool ... ok
test_seq ... ok
test_translate ... ok
Bio docstring test ... ok
Bio.Affy docstring test ... ok
Bio.Affy.CelFile docstring test ... ok
Bio.Align docstring test ... ok
Bio.Align.AlignInfo docstring test ... ok
Bio.Align.Applications docstring test ... ok
Bio.Align.Applications._ClustalOmega docstring test ... ok
Bio.Align.Applications._Clustalw docstring test ... ok
Bio.Align.Applications._Dialign docstring test ... ok
Bio.Align.Applications._MSAProbs docstring test ... ok
Bio.Align.Applications._Mafft docstring test ... ok
Bio.Align.Applications._Muscle docstring test ... ok
Bio.Align.Applications._Prank docstring test ... ok
Bio.Align.Applications._Probcons docstring test ... ok
Bio.Align.Applications._TCoffee docstring test ... ok
Bio.Align._aligners docstring test ... ok
Bio.Align.a2m docstring test ... ok
Bio.Align.bed docstring test ... ok
Bio.Align.bigbed docstring test ... ok
Bio.Align.bigmaf docstring test ... ok
Bio.Align.bigpsl docstring test ... ok
Bio.Align.clustal docstring test ... ok
Bio.Align.emboss docstring test ... ok
Bio.Align.exonerate docstring test ... ok
Bio.Align.fasta docstring test ... ok
Bio.Align.hhr docstring test ... ok
Bio.Align.interfaces docstring test ... ok
Bio.Align.maf docstring test ... ok
Bio.Align.mauve docstring test ... ok
Bio.Align.msf docstring test ... ok
Bio.Align.nexus docstring test ... ok
Bio.Align.phylip docstring test ... ok
Bio.Align.psl docstring test ... ok
Bio.Align.sam docstring test ... ok
Bio.Align.stockholm docstring test ... ok
Bio.Align.substitution_matrices docstring test ... ok
Bio.Align.tabular docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.ClustalIO docstring test ... ok
Bio.AlignIO.EmbossIO docstring test ... ok
Bio.AlignIO.FastaIO docstring test ... ok
Bio.AlignIO.Interfaces docstring test ... ok
Bio.AlignIO.MafIO docstring test ... ok
Bio.AlignIO.MauveIO docstring test ... ok
Bio.AlignIO.MsfIO docstring test ... ok
Bio.AlignIO.NexusIO docstring test ... ok
Bio.AlignIO.PhylipIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Application docstring test ... ok
Bio.Blast docstring test ... ok
Bio.Blast.Applications docstring test ... ok
Bio.Blast.NCBIWWW docstring test ... ok
Bio.Blast.NCBIXML docstring test ... ok
Bio.Blast.ParseBlastTable docstring test ... ok
Bio.Blast.Record docstring test ... ok
Bio.CAPS docstring test ... ok
Bio.Cluster docstring test ... ok
Bio.Cluster._cluster docstring test ... ok
Bio.Compass docstring test ... ok
Bio.Data docstring test ... ok
Bio.Data.CodonTable docstring test ... ok
Bio.Data.IUPACData docstring test ... ok
Bio.Data.PDBData docstring test ... ok
Bio.Data.SCOPData docstring test ... ok
Bio.Emboss docstring test ... ok
Bio.Emboss.Applications docstring test ... ok
Bio.Emboss.Primer3 docstring test ... ok
Bio.Emboss.PrimerSearch docstring test ... ok
Bio.Entrez.Parser docstring test ... ok
Bio.ExPASy.Enzyme docstring test ... ok
Bio.ExPASy.Prodoc docstring test ... ok
Bio.ExPASy.Prosite docstring test ... ok
Bio.ExPASy.ScanProsite docstring test ... ok
Bio.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.ccealign docstring test ... ok
Bio.PDB.cealign docstring test ... ok
Bio.PDB.ic_data docstring test ... ok
Bio.PDB.ic_rebuild docstring test ... ok
Bio.PDB.internal_coords docstring test ... ok
Bio.PDB.kdtrees docstring test ... ok
Bio.PDB.mmcifio docstring test ... ok
Bio.PDB.mmtf docstring test ... ok
Bio.PDB.mmtf.DefaultParser docstring test ... ok
Bio.PDB.mmtf.mmtfio docstring test ... ok
Bio.PDB.parse_pdb_header docstring test ... ok
Bio.PDB.qcprot docstring test ... ok
Bio.PDB.vectors docstring test ... ok
Bio.Pathway docstring test ... ok
Bio.Pathway.Rep docstring test ... ok
Bio.Pathway.Rep.Graph docstring test ... ok
Bio.Pathway.Rep.MultiGraph docstring test ... ok
Bio.Phylo docstring test ... ok
Bio.Phylo.Applications docstring test ... ok
Bio.Phylo.Applications._Fasttree docstring test ... ok
Bio.Phylo.Applications._Phyml docstring test ... ok
Bio.Phylo.Applications._Raxml docstring test ... ok
Bio.Phylo.BaseTree docstring test ... ok
Bio.Phylo.CDAO docstring test ... ok
Bio.Phylo.CDAOIO docstring test ... ok
Bio.Phylo.Consensus docstring test ... ok
Bio.Phylo.NeXML docstring test ... ok
Bio.Phylo.NeXMLIO docstring test ... ok
Bio.Phylo.Newick docstring test ... ok
Bio.Phylo.NewickIO docstring test ... ok
Bio.Phylo.NexusIO docstring test ... ok
Bio.Phylo.PAML docstring test ... ok
Bio.Phylo.PAML._paml docstring test ... ok
Bio.Phylo.PAML._parse_baseml docstring test ... ok
Bio.Phylo.PAML._parse_codeml docstring test ... ok
Bio.Phylo.PAML._parse_yn00 docstring test ... ok
Bio.Phylo.PAML.baseml docstring test ... ok
Bio.Phylo.PAML.chi2 docstring test ... ok
Bio.Phylo.PAML.codeml docstring test ... ok
Bio.Phylo.PAML.yn00 docstring test ... ok
Bio.Phylo.PhyloXML docstring test ... ok
Bio.Phylo.PhyloXMLIO docstring test ... ok
Bio.Phylo.TreeConstruction docstring test ... ok
Bio.Phylo._cdao_owl docstring test ... ok
Bio.Phylo._io docstring test ... ok
Bio.Phylo._utils docstring test ... ok
Bio.PopGen docstring test ... ok
Bio.PopGen.GenePop docstring test ... ok
Bio.PopGen.GenePop.Controller docstring test ... ok
Bio.PopGen.GenePop.EasyController docstring test ... ok
Bio.PopGen.GenePop.FileParser docstring test ... ok
Bio.PopGen.GenePop.LargeFileParser docstring test ... ok
Bio.Restriction docstring test ... ok
Bio.Restriction.PrintFormat docstring test ... ok
Bio.Restriction.Restriction docstring test ... ok
Bio.Restriction.Restriction_Dictionary docstring test ... ok
Bio.SCOP docstring test ... ok
Bio.SCOP.Cla docstring test ... ok
Bio.SCOP.Des docstring test ... ok
Bio.SCOP.Dom docstring test ... ok
Bio.SCOP.Hie docstring test ... ok
Bio.SCOP.Raf docstring test ... ok
Bio.SCOP.Residues docstring test ... ok
Bio.SVDSuperimposer docstring test ... ok
Bio.SearchIO docstring test ... ok
Bio.SearchIO.BlastIO docstring test ... ok
Bio.SearchIO.BlastIO.blast_tab docstring test ... ok
Bio.SearchIO.BlastIO.blast_text docstring test ... ok
Bio.SearchIO.BlastIO.blast_xml docstring test ... ok
Bio.SearchIO.BlatIO docstring test ... ok
Bio.SearchIO.ExonerateIO docstring test ... ok
Bio.SearchIO.ExonerateIO._base docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... ok
Bio.SearchIO.FastaIO docstring test ... ok
Bio.SearchIO.HHsuiteIO docstring test ... ok
Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... ok
Bio.SearchIO.HmmerIO docstring test ... ok
Bio.SearchIO.HmmerIO._base docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... ok
Bio.SearchIO.InterproscanIO docstring test ... ok
Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... ok
Bio.SearchIO._index docstring test ... ok
Bio.SearchIO._legacy docstring test ... ok
Bio.SearchIO._legacy.NCBIStandalone docstring test ... ok
Bio.SearchIO._legacy.ParserSupport docstring test ... ok
Bio.SearchIO._model docstring test ... ok
Bio.SearchIO._model._base docstring test ... ok
Bio.SearchIO._model.hit docstring test ... ok
Bio.SearchIO._model.hsp docstring test ... ok
Bio.SearchIO._model.query docstring test ... ok
Bio.SearchIO._utils docstring test ... ok
Bio.Seq docstring test ... ok
Bio.SeqFeature docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.AbiIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqIO.FastaIO docstring test ... ok
Bio.SeqIO.GckIO docstring test ... ok
Bio.SeqIO.IgIO docstring test ... ok
Bio.SeqIO.InsdcIO docstring test ... ok
Bio.SeqIO.Interfaces docstring test ... ok
Bio.SeqIO.NibIO docstring test ... ok
Bio.SeqIO.PdbIO docstring test ... ok
Bio.SeqIO.PhdIO docstring test ... ok
Bio.SeqIO.PirIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.SeqXmlIO docstring test ... ok
Bio.SeqIO.SffIO docstring test ... ok
Bio.SeqIO.SnapGeneIO docstring test ... ok
Bio.SeqIO.SwissIO docstring test ... ok
Bio.SeqIO.TabIO docstring test ... ok
Bio.SeqIO.TwoBitIO docstring test ... ok
Bio.SeqIO.UniprotIO docstring test ... ok
Bio.SeqIO.XdnaIO docstring test ... ok
Bio.SeqIO._index docstring test ... ok
Bio.SeqIO._twoBitIO docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.SeqUtils.CheckSum docstring test ... ok
Bio.SeqUtils.CodonUsage docstring test ... ok
Bio.SeqUtils.CodonUsageIndices docstring test ... ok
Bio.SeqUtils.IsoelectricPoint docstring test ... ok
Bio.SeqUtils.MeltingTemp docstring test ... ok
Bio.SeqUtils.ProtParam docstring test ... ok
Bio.SeqUtils.ProtParamData docstring test ... ok
Bio.SeqUtils.lcc docstring test ... ok
Bio.Sequencing docstring test ... ok
Bio.Sequencing.Ace docstring test ... ok
Bio.Sequencing.Applications docstring test ... ok
Bio.Sequencing.Applications._Novoalign docstring test ... ok
Bio.Sequencing.Applications._bwa docstring test ... ok
Bio.Sequencing.Applications._samtools docstring test ... ok
Bio.Sequencing.Phd docstring test ... ok
Bio.SwissProt docstring test ... ok
Bio.SwissProt.KeyWList docstring test ... ok
Bio.UniGene docstring test ... ok
Bio.UniProt docstring test ... ok
Bio.UniProt.GOA docstring test ... ok
Bio.Wise docstring test ... ok
Bio.Wise.dnal docstring test ... ok
Bio.Wise.psw docstring test ... ok
Bio._utils docstring test ... ok
Bio.bgzf docstring test ... ok
Bio.codonalign docstring test ... ok
Bio.codonalign.codonalignment docstring test ... ok
Bio.codonalign.codonseq docstring test ... ok
Bio.cpairwise2 docstring test ... ok
Bio.kNN docstring test ... ok
Bio.motifs docstring test ... ok
Bio.motifs._pwm docstring test ... ok
Bio.motifs.alignace docstring test ... ok
Bio.motifs.applications docstring test ... ok
Bio.motifs.applications._xxmotif docstring test ... ok
Bio.motifs.clusterbuster docstring test ... ok
Bio.motifs.jaspar docstring test ... ok
Bio.motifs.jaspar.db docstring test ... ok
Bio.motifs.mast docstring test ... ok
Bio.motifs.matrix docstring test ... ok
Bio.motifs.meme docstring test ... ok
Bio.motifs.minimal docstring test ... ok
Bio.motifs.pfm docstring test ... ok
Bio.motifs.thresholds docstring test ... ok
Bio.motifs.transfac docstring test ... ok
Bio.motifs.xms docstring test ... ok
Bio.pairwise2 docstring test ... ok
Bio.phenotype docstring test ... ok
Bio.phenotype.phen_micro docstring test ... ok
Bio.phenotype.pm_fitting docstring test ... ok
BioSQL docstring test ... ok
BioSQL.BioSeq docstring test ... ok
BioSQL.BioSeqDatabase docstring test ... ok
BioSQL.DBUtils docstring test ... ok
BioSQL.Loader docstring test ... ok
----------------------------------------------------------------------
Ran 553 tests in 1348.234 seconds

Skipping any tests requiring internet access
Python version: 3.10.9 (main, Dec  7 2022, 13:47:07) [GCC 12.2.0]
Operating system: posix linux
	rm -fr -- /tmp/dh-xdg-rundir-IzMvXxja
dh_auto_test: error: pybuild --test -i python{version} -p "3.11 3.10" --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" returned exit code 13
make[1]: *** [debian/rules:84: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/python-biopython-1.80+dfsg'
make: *** [debian/rules:42: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2022-12-26T12:17:50Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 333476
Build-Time: 3047
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 2041
Job: python-biopython_1.80+dfsg-3
Machine Architecture: armhf
Package: python-biopython
Package-Time: 5111
Source-Version: 1.80+dfsg-3
Space: 333476
Status: attempted
Version: 1.80+dfsg-3
--------------------------------------------------------------------------------
Finished at 2022-12-26T12:17:50Z
Build needed 01:25:11, 333476k disk space

Page generated on 2024-05-17 22:06:04 UTC
Pages written by Mehdi Dogguy
Architecture specific issues should be sent to <$arch@buildd.debian.org>
Service maintained by the wanna-build team <debian-wb-team@lists.debian.org>
Download code with git: git clone https://buildd.debian.org/git/pgstatus.git
Valid XHTML  Valid CSS