Raspbian Package Auto-Building

genometools → 1.5.9+ds-2 → armhf → 2016-07-29 13:45:28

sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard

+==============================================================================+
| genometools 1.5.9+ds-2 (armhf)                             29 Jul 2016 11:34 |
+==============================================================================+

Package: genometools
Version: 1.5.9+ds-2
Source Version: 1.5.9+ds-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/genometools-JZUZMT/genometools-1.5.9+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/genometools-JZUZMT' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-8fbd04cf-b271-46f5-8386-9ac41699de58' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9180 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.1 MB]
Fetched 20.3 MB in 1min 27s (232 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'genometools' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/genometools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/genometools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 7800 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main genometools 1.5.9+ds-2 (dsc) [3500 B]
Get:2 http://172.17.0.1/private stretch-staging/main genometools 1.5.9+ds-2 (tar) [7775 kB]
Get:3 http://172.17.0.1/private stretch-staging/main genometools 1.5.9+ds-2 (diff) [20.8 kB]
Fetched 7800 kB in 25s (310 kB/s)
Download complete and in download only mode

Check architectures
-------------------


Check dependencies
------------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-1bt380/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ Sources [194 B]
Get:5 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ Packages [506 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-1bt380/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 48 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-1bt380/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 13893 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.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
Merged Build-Depends: debhelper (>= 9), dh-python, liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, libtre-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python, asciidoc, libxml2-utils, xsltproc, ruby, docbook-xsl, faketime, imagemagick
Filtered Build-Depends: debhelper (>= 9), dh-python, liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, libtre-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python, asciidoc, libxml2-utils, xsltproc, ruby, docbook-xsl, faketime, imagemagick
dpkg-deb: building package 'sbuild-build-depends-genometools-dummy' in '/<<BUILDDIR>>/resolver-SnryF5/apt_archive/sbuild-build-depends-genometools-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ Sources [365 B]
Get:5 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ Packages [687 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-SnryF5/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...

+------------------------------------------------------------------------------+
| Install genometools build dependencies (apt-based resolver)                  |
+------------------------------------------------------------------------------+

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  asciidoc autoconf automake autopoint autotools-dev bsdmainutils
  ca-certificates debhelper dh-autoreconf dh-python dh-strip-nondeterminism
  docbook-xsl faketime file fontconfig fontconfig-config fonts-cabin
  fonts-comfortaa fonts-crosextra-caladea fonts-crosextra-carlito
  fonts-dejavu-core fonts-dejavu-extra fonts-ebgaramond fonts-ebgaramond-extra
  fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
  fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine
  fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto-hinted
  fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus
  fonts-sil-gentiumplus-compact fonts-stix gettext gettext-base
  gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base
  hicolor-icon-theme icu-devtools imagemagick imagemagick-6.q16
  imagemagick-common intltool-debian libarchive-zip-perl libavahi-client3
  libavahi-common-data libavahi-common3 libbam-dev libbsd0 libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcroco3 libcups2 libcupsfilters1 libcupsimage2 libdatrie1 libelf1
  libexpat1 libexpat1-dev libfaketime libffi6 libfftw3-double3
  libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
  libfreetype6 libfreetype6-dev libgirepository-1.0-1 libglib2.0-0
  libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls30 libgraphite2-3
  libgraphite2-dev libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-dev
  libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhogweed4 libice-dev
  libice6 libicu-dev libicu55 libijs-0.35 libjbig0 libjbig2dec0
  libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3
  libkrb5support0 liblcms2-2 libldap-2.4-2 liblqr-1-0 libltdl7 liblua5.1-0
  liblua5.1-0-dev liblzo2-2 libmagic1 libmagickcore-6.q16-2
  libmagickwand-6.q16-2 libmpdec2 libncurses5 libncursesw5 libnettle6 libnspr4
  libnss3 libopenjp2-7 libp11-kit0 libpango-1.0-0 libpango1.0-dev
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils
  libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1
  libpixman-1-0 libpixman-1-dev libpng-dev libpng16-16 libpoppler61
  libpotrace0 libptexenc1 libpthread-stubs0-dev libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
  libpython3.5-minimal libpython3.5-stdlib libreadline-dev libreadline6-dev
  libruby2.3 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm-dev libsm6
  libsqlite3-0 libsqlite3-dev libssl1.0.2 libsynctex1 libtasn1-6 libtexlua52
  libtexluajit2 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev
  libtinfo5 libtool libtre-dev libtre5 libunistring0 libx11-6 libx11-data
  libx11-dev libxau-dev libxau6 libxaw7 libxcb-render0 libxcb-render0-dev
  libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6
  libxext-dev libxext6 libxft-dev libxft2 libxi6 libxml2 libxml2-utils libxmu6
  libxpm4 libxrender-dev libxrender1 libxslt1.1 libxt6 libyaml-0-2
  libzzip-0-13 lua-filesystem lua-filesystem-dev lua-lpeg lua-lpeg-dev lua-md5
  lua-md5-dev m4 man-db mime-support openssl pkg-config po-debconf
  poppler-data preview-latex-style python python-minimal python2.7
  python2.7-minimal python3 python3-minimal python3.5 python3.5-minimal rake
  ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
  ruby-test-unit ruby2.3 rubygems-integration sgml-base t1utils tex-common
  texlive-base texlive-binaries texlive-fonts-extra texlive-fonts-recommended
  texlive-latex-base texlive-latex-extra texlive-latex-recommended
  texlive-pictures ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ucf
  x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev
  x11proto-render-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools
  xsltproc xtrans-dev zlib1g-dev
Suggested packages:
  source-highlight vim-addon-manager autoconf-archive gnu-standards
  autoconf-doc wamerican | wordlist whois vacation dh-make dbtoepub
  docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text
  | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java
  libxslthl-java xalan fontforge gettext-doc libasprintf-dev libgettextpo-dev
  groff 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 libcairo2-doc cups-common libfftw3-bin
  libfftw3-dev libglib2.0-doc gnutls-bin krb5-doc krb5-user libice-doc icu-doc
  liblcms2-utils libmagickcore-6.q16-2-extra libpango1.0-doc readline-doc
  libsm-doc sqlite3-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
  tre-agrep libxcb-doc libxext-doc less www-browser libmail-box-perl
  poppler-utils ghostscript fonts-japanese-mincho | fonts-ipafont-mincho
  fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai
  fonts-arphic-uming fonts-nanum python-doc python-tk python2.7-doc
  binfmt-support python3-doc python3-tk python3-venv python3.5-venv
  python3.5-doc ri ruby-dev bundler sgml-base-doc perl-tk xpdf-reader
  | pdf-viewer gv | postscript-viewer cm-super libspreadsheet-parseexcel-perl
  libfile-which-perl python-pygments texlive-pstricks libtcltk-ruby dot2tex
  prerex gvfs-bin
Recommended packages:
  dblatex docbook-utils xmlto docbook-xml curl | wget | lynx-cur
  libmagickcore-6.q16-2-extra ghostscript netpbm bzip2-doc shared-mime-info
  xdg-user-dirs fonts-droid-fallback krb5-locales libtool-bin gsfonts libgpm2
  libpng-tools libsasl2-modules libltdl-dev libx11-doc libmail-sendmail-perl
  zip libjs-jquery lmodern wish texlive-fonts-extra-doc tex-gyre
  texlive-fonts-recommended-doc tipa texlive-latex-base-doc
  texlive-latex-extra-doc prosper texlive-latex-recommended-doc tk
  texlive-pictures-doc libfile-mimeinfo-perl libnet-dbus-perl
  libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  asciidoc autoconf automake autopoint autotools-dev bsdmainutils
  ca-certificates debhelper dh-autoreconf dh-python dh-strip-nondeterminism
  docbook-xsl faketime file fontconfig fontconfig-config fonts-cabin
  fonts-comfortaa fonts-crosextra-caladea fonts-crosextra-carlito
  fonts-dejavu-core fonts-dejavu-extra fonts-ebgaramond fonts-ebgaramond-extra
  fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
  fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine
  fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto-hinted
  fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus
  fonts-sil-gentiumplus-compact fonts-stix gettext gettext-base
  gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base
  hicolor-icon-theme icu-devtools imagemagick imagemagick-6.q16
  imagemagick-common intltool-debian libarchive-zip-perl libavahi-client3
  libavahi-common-data libavahi-common3 libbam-dev libbsd0 libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcroco3 libcups2 libcupsfilters1 libcupsimage2 libdatrie1 libelf1
  libexpat1 libexpat1-dev libfaketime libffi6 libfftw3-double3
  libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
  libfreetype6 libfreetype6-dev libgirepository-1.0-1 libglib2.0-0
  libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls30 libgraphite2-3
  libgraphite2-dev libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-dev
  libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhogweed4 libice-dev
  libice6 libicu-dev libicu55 libijs-0.35 libjbig0 libjbig2dec0
  libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3
  libkrb5support0 liblcms2-2 libldap-2.4-2 liblqr-1-0 libltdl7 liblua5.1-0
  liblua5.1-0-dev liblzo2-2 libmagic1 libmagickcore-6.q16-2
  libmagickwand-6.q16-2 libmpdec2 libnettle6 libnspr4 libnss3 libopenjp2-7
  libp11-kit0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0
  libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre16-3
  libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0
  libpixman-1-dev libpng-dev libpng16-16 libpoppler61 libpotrace0 libptexenc1
  libpthread-stubs0-dev libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal
  libpython3.5-stdlib libreadline-dev libreadline6-dev libruby2.3 libsasl2-2
  libsasl2-modules-db libsigsegv2 libsm-dev libsm6 libsqlite3-0 libsqlite3-dev
  libssl1.0.2 libsynctex1 libtasn1-6 libtexlua52 libtexluajit2 libthai-data
  libthai0 libtiff5 libtimedate-perl libtinfo-dev libtool libtre-dev libtre5
  libunistring0 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxaw7
  libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb1
  libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxft-dev libxft2
  libxi6 libxml2 libxml2-utils libxmu6 libxpm4 libxrender-dev libxrender1
  libxslt1.1 libxt6 libyaml-0-2 libzzip-0-13 lua-filesystem lua-filesystem-dev
  lua-lpeg lua-lpeg-dev lua-md5 lua-md5-dev m4 man-db mime-support openssl
  pkg-config po-debconf poppler-data preview-latex-style python python-minimal
  python2.7 python2.7-minimal python3 python3-minimal python3.5
  python3.5-minimal rake ruby ruby-did-you-mean ruby-minitest ruby-net-telnet
  ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration
  sbuild-build-depends-genometools-dummy sgml-base t1utils tex-common
  texlive-base texlive-binaries texlive-fonts-extra texlive-fonts-recommended
  texlive-latex-base texlive-latex-extra texlive-latex-recommended
  texlive-pictures ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ucf
  x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev
  x11proto-render-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools
  xsltproc xtrans-dev zlib1g-dev
The following packages will be upgraded:
  libncurses5 libncursesw5 libtinfo5
3 upgraded, 267 newly installed, 0 to remove and 45 not upgraded.
Need to get 406 MB/414 MB of archives.
After this operation, 1276 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-SnryF5/apt_archive ./ sbuild-build-depends-genometools-dummy 0.invalid.0 [948 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libtinfo5 armhf 6.0+20160625-1 [285 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libncurses5 armhf 6.0+20160625-1 [73.9 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libncursesw5 armhf 6.0+20160625-1 [93.3 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-1 [387 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-1 [1167 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.13.0-1 [479 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2h-1 [889 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-1 [1844 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-1 [276 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.23-1 [260 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.36-1 [1068 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.4 [271 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.4 [313 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf fontconfig armhf 2.11.0-6.4 [401 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf fonts-lato all 2.0-1 [2684 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf imagemagick-common all 8:6.8.9.9-7.2 [149 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libfftw3-double3 armhf 3.3.4-2+rvt+b1 [437 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-2 [2546 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf liblqr-1-0 armhf 0.4.2-2 [20.9 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.0-1 [109 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.7-1 [116 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.6-0.1 [42.8 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-2 [203 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1 [40.9 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1 [804 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libmagickcore-6.q16-2 armhf 8:6.8.9.9-7.2 [1516 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libmagickwand-6.q16-2 armhf 8:6.8.9.9-7.2 [378 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libpcrecpp0v5 armhf 2:8.38-3.1 [148 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libtre5 armhf 0.8.0-4 [51.3 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libxft2 armhf 2.3.2-1 [48.3 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libyaml-0-2 armhf 0.1.6-3 [41.5 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libzzip-0-13 armhf 0.13.62-3 [51.3 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf lua-md5 armhf 1.2+git+1+8d87fee-1 [14.6 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf lua-md5-dev armhf 1.2+git+1+8d87fee-1 [22.3 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf poppler-data all 0.4.7-7 [1466 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-minimal armhf 3.5.2-2 [562 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf python3.5-minimal armhf 3.5.2-2 [1424 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf python3-minimal armhf 3.5.1-4 [35.3 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-stdlib armhf 3.5.2-2 [2082 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf python3.5 armhf 3.5.2-2 [210 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libpython3-stdlib armhf 3.5.1-4 [18.6 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf dh-python all 2.20160721 [82.2 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf python3 armhf 3.5.1-4 [21.7 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf sgml-base all 1.28 [14.7 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-2 [269 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-2 [62.4 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.8-1 [44.1 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.4.14-1 [737 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.2+dfsg-1 [57.2 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.2+dfsg-1 [111 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.2+dfsg-1 [261 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.2+dfsg-1 [131 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-15 [65.6 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.26.dfsg1-15 [96.7 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1+b2 [198 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf asciidoc all 8.6.9-3 [830 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2h-1 [667 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.019-1 [12.2 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.019-1 [7352 B]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160709 [799 kB]
Get:102 http://172.17.0.1/private stretch-staging/main armhf docbook-xsl all 1.79.1+dfsg-1 [1249 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf fonts-cabin all 1.5-2 [139 kB]
Get:104 http://172.17.0.1/private stretch-staging/main armhf fonts-comfortaa all 2.003-1 [133 kB]
Get:105 http://172.17.0.1/private stretch-staging/main armhf fonts-crosextra-caladea all 20130214-1 [82.1 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf fonts-crosextra-carlito all 20130920-1 [745 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-extra all 2.36-1 [1314 kB]
Get:108 http://172.17.0.1/private stretch-staging/main armhf fonts-ebgaramond all 0.015+git20130628-3 [415 kB]
Get:109 http://172.17.0.1/private stretch-staging/main armhf fonts-ebgaramond-extra all 0.015+git20130628-3 [680 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf fonts-font-awesome all 4.6.3~dfsg-1 [550 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf fonts-freefont-otf all 20120503-4 [3186 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf fonts-freefont-ttf all 20120503-4 [4262 kB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-artemisia all 1.1-5 [259 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-complutum all 1.1-6 [41.6 kB]
Get:115 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-didot all 1.1-6 [278 kB]
Get:116 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-neohellenic all 1.1-6 [215 kB]
Get:117 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-olga all 1.1-5 [33.2 kB]
Get:118 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-solomos all 1.1-5 [40.6 kB]
Get:119 http://172.17.0.1/private stretch-staging/main armhf fonts-junicode all 0.7.8-2 [643 kB]
Get:120 http://172.17.0.1/private stretch-staging/main armhf fonts-linuxlibertine all 5.3.0-2 [1713 kB]
Get:121 http://172.17.0.1/private stretch-staging/main armhf fonts-lobster all 2.0-2 [39.5 kB]
Get:122 http://172.17.0.1/private stretch-staging/main armhf fonts-lobstertwo all 2.0-2 [94.0 kB]
Get:123 http://172.17.0.1/private stretch-staging/main armhf fonts-oflb-asana-math all 000.907-6 [245 kB]
Get:124 http://172.17.0.1/private stretch-staging/main armhf fonts-roboto-hinted all 2:0~20160106-1 [2931 kB]
Get:125 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentium all 20081126:1.03-1 [251 kB]
Get:126 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentium-basic all 1.1-7 [382 kB]
Get:127 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentiumplus all 5.000-1 [2811 kB]
Get:128 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentiumplus-compact all 5.000-2 [1522 kB]
Get:129 http://172.17.0.1/private stretch-staging/main armhf libgirepository-1.0-1 armhf 1.48.0-3 [84.1 kB]
Get:130 http://172.17.0.1/private stretch-staging/main armhf gir1.2-glib-2.0 armhf 1.48.0-3 [145 kB]
Get:131 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-0 armhf 0.33.6-1 [454 kB]
Get:132 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.11.1-1 [17.0 kB]
Get:133 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0 armhf 1.11.1-1 [11.5 kB]
Get:134 http://172.17.0.1/private stretch-staging/main armhf libcairo2 armhf 1.14.6-1+b1 [686 kB]
Get:135 http://172.17.0.1/private stretch-staging/main armhf libcairo-gobject2 armhf 1.14.6-1+b1 [332 kB]
Get:136 http://172.17.0.1/private stretch-staging/main armhf gir1.2-freedesktop armhf 1.48.0-3 [22.9 kB]
Get:137 http://172.17.0.1/private stretch-staging/main armhf libthai-data all 0.1.25-1 [165 kB]
Get:138 http://172.17.0.1/private stretch-staging/main armhf libdatrie1 armhf 0.2.10-2 [32.5 kB]
Get:139 http://172.17.0.1/private stretch-staging/main armhf libthai0 armhf 0.1.25-1 [48.5 kB]
Get:140 http://172.17.0.1/private stretch-staging/main armhf libpango-1.0-0 armhf 1.40.1-1 [293 kB]
Get:141 http://172.17.0.1/private stretch-staging/main armhf libgraphite2-3 armhf 1.3.8-1 [62.5 kB]
Get:142 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz0b armhf 1.2.7-1 [587 kB]
Get:143 http://172.17.0.1/private stretch-staging/main armhf libpangoft2-1.0-0 armhf 1.40.1-1 [231 kB]
Get:144 http://172.17.0.1/private stretch-staging/main armhf libpangocairo-1.0-0 armhf 1.40.1-1 [220 kB]
Get:145 http://172.17.0.1/private stretch-staging/main armhf libpangoxft-1.0-0 armhf 1.40.1-1 [215 kB]
Get:146 http://172.17.0.1/private stretch-staging/main armhf gir1.2-pango-1.0 armhf 1.40.1-1 [224 kB]
Get:147 http://172.17.0.1/private stretch-staging/main armhf hicolor-icon-theme all 0.15-1 [9550 B]
Get:148 http://172.17.0.1/private stretch-staging/main armhf icu-devtools armhf 55.1-7 [163 kB]
Get:149 http://172.17.0.1/private stretch-staging/main armhf imagemagick-6.q16 armhf 8:6.8.9.9-7.2 [500 kB]
Get:150 http://172.17.0.1/private stretch-staging/main armhf imagemagick armhf 8:6.8.9.9-7.2 [156 kB]
Get:151 http://172.17.0.1/private stretch-staging/main armhf libavahi-common-data armhf 0.6.32-1 [118 kB]
Get:152 http://172.17.0.1/private stretch-staging/main armhf libavahi-common3 armhf 0.6.32-1 [48.6 kB]
Get:153 http://172.17.0.1/private stretch-staging/main armhf libavahi-client3 armhf 0.6.32-1 [51.2 kB]
Get:154 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:155 http://172.17.0.1/private stretch-staging/main armhf libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:156 http://172.17.0.1/private stretch-staging/main armhf libcairo-script-interpreter2 armhf 1.14.6-1+b1 [361 kB]
Get:157 http://172.17.0.1/private stretch-staging/main armhf libexpat1-dev armhf 2.2.0-1 [117 kB]
Get:158 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:159 http://172.17.0.1/private stretch-staging/main armhf libpng-dev armhf 1.6.23-1 [228 kB]
Get:160 http://172.17.0.1/private stretch-staging/main armhf libfreetype6-dev armhf 2.6.3-3+b1 [5757 kB]
Get:161 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1-dev armhf 2.11.0-6.4 [875 kB]
Get:162 http://172.17.0.1/private stretch-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:163 http://172.17.0.1/private stretch-staging/main armhf x11proto-core-dev all 7.0.29-1 [728 kB]
Get:164 http://172.17.0.1/private stretch-staging/main armhf libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:165 http://172.17.0.1/private stretch-staging/main armhf libxdmcp-dev armhf 1:1.1.2-1.1 [40.8 kB]
Get:166 http://172.17.0.1/private stretch-staging/main armhf x11proto-input-dev all 2.3.2-1 [158 kB]
Get:167 http://172.17.0.1/private stretch-staging/main armhf x11proto-kb-dev all 1.0.7-1 [233 kB]
Get:168 http://172.17.0.1/private stretch-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:169 http://172.17.0.1/private stretch-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:170 http://172.17.0.1/private stretch-staging/main armhf libxcb1-dev armhf 1.11.1-1 [75.9 kB]
Get:171 http://172.17.0.1/private stretch-staging/main armhf libx11-dev armhf 2:1.6.3-1 [749 kB]
Get:172 http://172.17.0.1/private stretch-staging/main armhf x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:173 http://172.17.0.1/private stretch-staging/main armhf libxrender-dev armhf 1:0.9.9-2 [36.5 kB]
Get:174 http://172.17.0.1/private stretch-staging/main armhf x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:175 http://172.17.0.1/private stretch-staging/main armhf libxext-dev armhf 2:1.3.3-1 [102 kB]
Get:176 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+16 [251 kB]
Get:177 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:178 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:179 http://172.17.0.1/private stretch-staging/main armhf libice-dev armhf 2:1.0.9-1+b1 [59.0 kB]
Get:180 http://172.17.0.1/private stretch-staging/main armhf libsm-dev armhf 2:1.2.2-1+b1 [33.5 kB]
Get:181 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-dev armhf 0.33.6-1 [476 kB]
Get:182 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0-dev armhf 1.11.1-1 [20.8 kB]
Get:183 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0-dev armhf 1.11.1-1 [12.6 kB]
Get:184 http://172.17.0.1/private stretch-staging/main armhf libelf1 armhf 0.166-2 [169 kB]
Get:185 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-data all 2.48.1-2 [2503 kB]
Get:186 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-bin armhf 2.48.1-2 [1624 kB]
Get:187 http://172.17.0.1/private stretch-staging/main armhf libpcre16-3 armhf 2:8.38-3.1 [229 kB]
Get:188 http://172.17.0.1/private stretch-staging/main armhf libpcre32-3 armhf 2:8.38-3.1 [223 kB]
Get:189 http://172.17.0.1/private stretch-staging/main armhf libpcre3-dev armhf 2:8.38-3.1 [556 kB]
Get:190 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-dev armhf 2.48.1-2 [2783 kB]
Get:191 http://172.17.0.1/private stretch-staging/main armhf libcairo2-dev armhf 1.14.6-1+b1 [812 kB]
Get:192 http://172.17.0.1/private stretch-staging/main armhf libcups2 armhf 2.1.4-4 [268 kB]
Get:193 http://172.17.0.1/private stretch-staging/main armhf libcupsimage2 armhf 2.1.4-4 [118 kB]
Get:194 http://172.17.0.1/private stretch-staging/main armhf libcupsfilters1 armhf 1.10.0-1 [117 kB]
Get:195 http://172.17.0.1/private stretch-staging/main armhf libgraphite2-dev armhf 1.3.8-1 [21.0 kB]
Get:196 http://172.17.0.1/private stretch-staging/main armhf libijs-0.35 armhf 0.35-12 [16.0 kB]
Get:197 http://172.17.0.1/private stretch-staging/main armhf libjbig2dec0 armhf 0.13-2 [51.1 kB]
Get:198 http://172.17.0.1/private stretch-staging/main armhf libopenjp2-7 armhf 2.1.1-1 [106 kB]
Get:199 http://172.17.0.1/private stretch-staging/main armhf libgs9-common all 9.19~dfsg-1 [3032 kB]
Get:200 http://172.17.0.1/private stretch-staging/main armhf libgs9 armhf 9.19~dfsg-1+b1 [1729 kB]
Get:201 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-icu0 armhf 1.2.7-1 [438 kB]
Get:202 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-gobject0 armhf 1.2.7-1 [443 kB]
Get:203 http://172.17.0.1/private stretch-staging/main armhf libicu-dev armhf 55.1-7 [8339 kB]
Get:204 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-dev armhf 1.2.7-1 [642 kB]
Get:205 http://172.17.0.1/private stretch-staging/main armhf libkpathsea6 armhf 2016.20160513.41080-4 [149 kB]
Get:206 http://172.17.0.1/private stretch-staging/main armhf liblua5.1-0 armhf 5.1.5-8 [83.3 kB]
Get:207 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20160625-1 [65.6 kB]
Get:208 http://172.17.0.1/private stretch-staging/main armhf libreadline6-dev armhf 6.3-8+b3 [105 kB]
Get:209 http://172.17.0.1/private stretch-staging/main armhf libreadline-dev armhf 6.3-8+b3 [958 B]
Get:210 http://172.17.0.1/private stretch-staging/main armhf liblua5.1-0-dev armhf 5.1.5-8 [115 kB]
Get:211 http://172.17.0.1/private stretch-staging/main armhf libnspr4 armhf 2:4.12-2 [94.1 kB]
Get:212 http://172.17.0.1/private stretch-staging/main armhf libnss3 armhf 2:3.23-2 [938 kB]
Get:213 http://172.17.0.1/private stretch-staging/main armhf libxft-dev armhf 2.3.2-1 [59.1 kB]
Get:214 http://172.17.0.1/private stretch-staging/main armhf libpango1.0-dev armhf 1.40.1-1 [453 kB]
Get:215 http://172.17.0.1/private stretch-staging/main armhf libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:216 http://172.17.0.1/private stretch-staging/main armhf libpoppler61 armhf 0.44.0-3 [1146 kB]
Get:217 http://172.17.0.1/private stretch-staging/main armhf libpotrace0 armhf 1.13-2 [22.8 kB]
Get:218 http://172.17.0.1/private stretch-staging/main armhf libptexenc1 armhf 2016.20160513.41080-4 [54.8 kB]
Get:219 http://172.17.0.1/private stretch-staging/main armhf rubygems-integration all 1.10 [4882 B]
Get:220 http://172.17.0.1/private stretch-staging/main armhf ruby2.3 armhf 2.3.1-2 [177 kB]
Get:221 http://172.17.0.1/private stretch-staging/main armhf ruby armhf 1:2.3.0+4 [10.6 kB]
Get:222 http://172.17.0.1/private stretch-staging/main armhf rake all 10.5.0-2 [49.4 kB]
Get:223 http://172.17.0.1/private stretch-staging/main armhf ruby-did-you-mean all 1.0.0-2 [11.2 kB]
Get:224 http://172.17.0.1/private stretch-staging/main armhf ruby-minitest all 5.9.0-1 [51.1 kB]
Get:225 http://172.17.0.1/private stretch-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:226 http://172.17.0.1/private stretch-staging/main armhf ruby-power-assert all 0.3.0-1 [7902 B]
Get:227 http://172.17.0.1/private stretch-staging/main armhf ruby-test-unit all 3.1.7-2 [69.6 kB]
Get:228 http://172.17.0.1/private stretch-staging/main armhf libruby2.3 armhf 2.3.1-2 [2846 kB]
Get:229 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-dev armhf 3.13.0-1 [621 kB]
Get:230 http://172.17.0.1/private stretch-staging/main armhf libsynctex1 armhf 2016.20160513.41080-4 [57.3 kB]
Get:231 http://172.17.0.1/private stretch-staging/main armhf libtexlua52 armhf 2016.20160513.41080-4 [84.7 kB]
Get:232 http://172.17.0.1/private stretch-staging/main armhf libtexluajit2 armhf 2016.20160513.41080-4 [202 kB]
Get:233 http://172.17.0.1/private stretch-staging/main armhf libtre-dev armhf 0.8.0-4 [27.1 kB]
Get:234 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:235 http://172.17.0.1/private stretch-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:236 http://172.17.0.1/private stretch-staging/main armhf libxpm4 armhf 1:3.5.11-1+b1 [42.4 kB]
Get:237 http://172.17.0.1/private stretch-staging/main armhf libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:238 http://172.17.0.1/private stretch-staging/main armhf libxi6 armhf 2:1.7.6-1 [75.9 kB]
Get:239 http://172.17.0.1/private stretch-staging/main armhf libxml2-utils armhf 2.9.4+dfsg1-1 [102 kB]
Get:240 http://172.17.0.1/private stretch-staging/main armhf libxslt1.1 armhf 1.1.28-4 [212 kB]
Get:241 http://172.17.0.1/private stretch-staging/main armhf lua-filesystem armhf 1.6.3-1 [9984 B]
Get:242 http://172.17.0.1/private stretch-staging/main armhf lua-filesystem-dev armhf 1.6.3-1 [24.4 kB]
Get:243 http://172.17.0.1/private stretch-staging/main armhf lua-lpeg armhf 0.12.2-1 [25.4 kB]
Get:244 http://172.17.0.1/private stretch-staging/main armhf lua-lpeg-dev armhf 0.12.2-1 [44.3 kB]
Get:245 http://172.17.0.1/private stretch-staging/main armhf tex-common all 6.05 [564 kB]
Get:246 http://172.17.0.1/private stretch-staging/main armhf preview-latex-style all 11.87-3+deb8u1 [318 kB]
Get:247 http://172.17.0.1/private stretch-staging/main armhf t1utils armhf 1.39-2 [52.7 kB]
Get:248 http://172.17.0.1/private stretch-staging/main armhf texlive-binaries armhf 2016.20160513.41080-4 [4906 kB]
Get:249 http://172.17.0.1/private stretch-staging/main armhf xdg-utils all 1.1.1-1 [71.1 kB]
Get:250 http://172.17.0.1/private stretch-staging/main armhf texlive-base all 2016.20160623-1 [15.6 MB]
Get:251 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-gillius all 0.20090423-2 [400 kB]
Get:252 http://172.17.0.1/private stretch-staging/main armhf fonts-stix all 1.1.1-4 [590 kB]
Get:253 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-accanthis all 0.20090423-2 [401 kB]
Get:254 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-universalis all 0.20090423-2 [221 kB]
Get:255 http://172.17.0.1/private stretch-staging/main armhf texlive-fonts-extra all 2016.20160623-1 [240 MB]
Get:256 http://172.17.0.1/private stretch-staging/main armhf texlive-fonts-recommended all 2016.20160623-1 [5685 kB]
Get:257 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-base all 2016.20160623-1 [872 kB]
Get:258 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-recommended all 2016.20160623-1 [13.0 MB]
Get:259 http://172.17.0.1/private stretch-staging/main armhf texlive-pictures all 2016.20160623-1 [3768 kB]
Get:260 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-extra all 2016.20160623-1 [10.4 MB]
Get:261 http://172.17.0.1/private stretch-staging/main armhf xsltproc armhf 1.1.28-4 [118 kB]
Get:262 http://172.17.0.1/private stretch-staging/main armhf libfaketime armhf 0.9.6-7 [25.0 kB]
Get:263 http://172.17.0.1/private stretch-staging/main armhf faketime armhf 0.9.6-7 [13.4 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up fonts-sil-gentium (20081126:1.03-1) ...
Setting up xdg-utils (1.1.1-1) ...
Setting up ca-certificates (20160104) ...
Setting up hicolor-icon-theme (0.15-1) ...
Setting up fonts-sil-gentium-basic (1.1-7) ...
Setting up libgraphite2-dev (1.3.8-1) ...
Setting up lua-lpeg:armhf (0.12.2-1) ...
Setting up libtexluajit2:armhf (2016.20160513.41080-4) ...
Setting up fonts-gfs-olga (1.1-5) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.12-1) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libmpdec2:armhf (2.4.2-1) ...
Setting up liblzo2-2:armhf (2.08-1.2) ...
Setting up ruby-power-assert (0.3.0-1) ...
Setting up libavahi-common-data:armhf (0.6.32-1) ...
Setting up fonts-roboto-hinted (2:0~20160106-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.019-1) ...
Setting up libpaper1:armhf (1.1.24+nmu4) ...

Creating config file /etc/papersize with new version
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libpcre3-dev:armhf (2:8.38-3.1) ...
Setting up fontconfig-config (2.11.0-6.4) ...
Setting up tex-common (6.05) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up x11proto-core-dev (7.0.29-1) ...
Setting up lua-md5-dev:armhf (1.2+git+1+8d87fee-1) ...
Setting up ruby-test-unit (3.1.7-2) ...
Setting up libsqlite3-dev:armhf (3.13.0-1) ...
Setting up liblua5.1-0-dev:armhf (5.1.5-8) ...
Setting up docbook-xsl (1.79.1+dfsg-1) ...
Setting up libglib2.0-0:armhf (2.48.1-2) ...
No schema files found: doing nothing.
Setting up libpython3.5-stdlib:armhf (3.5.2-2) ...
Setting up fonts-lobstertwo (2.0-2) ...
Setting up libxml2-utils (2.9.4+dfsg1-1) ...
Setting up python2.7 (2.7.12-1) ...
Setting up libnss3:armhf (2:3.23-2) ...
Setting up libharfbuzz0b:armhf (1.2.7-1) ...
Setting up libxau-dev:armhf (1:1.0.8-1) ...
Setting up xsltproc (1.1.28-4) ...
Setting up preview-latex-style (11.87-3+deb8u1) ...
update-language: texlive-base not installed and configured, doing nothing!
Regenerating '/var/lib/texmf/fmtutil.cnf-DEBIAN'... done.
Regenerating '/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST'... done.
update-fmtutil has updated the following file(s):
	/var/lib/texmf/fmtutil.cnf-DEBIAN
	/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST
If you want to activate the changes in the above file(s),
you should run fmtutil-sys or fmtutil.
Setting up autoconf (2.69-10) ...
Setting up libthai0:armhf (0.1.25-1) ...
Setting up lua-lpeg-dev:armhf (0.12.2-1) ...
Setting up libicu-dev:armhf (55.1-7) ...
Setting up file (1:5.28-2) ...
Setting up libkrb5support0:armhf (1.14.2+dfsg-1) ...
Setting up libgirepository-1.0-1:armhf (1.48.0-3) ...
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up pkg-config (0.29-4) ...
Setting up liblqr-1-0:armhf (0.4.2-2) ...
Setting up gir1.2-glib-2.0:armhf (1.48.0-3) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-1.1) ...
Setting up libp11-kit0:armhf (0.23.2-3) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libice6:armhf (2:1.0.9-1+b1) ...
Setting up rubygems-integration (1.10) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libavahi-common3:armhf (0.6.32-1) ...
Setting up libpng-dev:armhf (1.6.23-1) ...
Setting up x11proto-render-dev (2:0.11.1-2) ...
Setting up libglib2.0-bin (2.48.1-2) ...
Setting up libxcb1:armhf (1.11.1-1) ...
Setting up x11proto-input-dev (2.3.2-1) ...
Setting up libharfbuzz-gobject0:armhf (1.2.7-1) ...
Setting up python (2.7.11-2) ...
Setting up libtool (2.4.6-0.1) ...
Setting up python3.5 (3.5.2-2) ...
Setting up libpython3-stdlib:armhf (3.5.1-4) ...
Setting up libfontconfig1:armhf (2.11.0-6.4) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up libk5crypto3:armhf (1.14.2+dfsg-1) ...
Setting up libxcb-render0:armhf (1.11.1-1) ...
Setting up libharfbuzz-icu0:armhf (1.2.7-1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libgnutls30:armhf (3.4.14-1) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up x11proto-xext-dev (7.3.0-1) ...
Setting up libfreetype6-dev (2.6.3-3+b1) ...
Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b2) ...
Setting up libice-dev:armhf (2:1.0.9-1+b1) ...
Setting up asciidoc (8.6.9-3) ...
Setting up libxcb-shm0:armhf (1.11.1-1) ...
Setting up libxpm4:armhf (1:3.5.11-1+b1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up libxcb1-dev:armhf (1.11.1-1) ...
Setting up libavahi-client3:armhf (0.6.32-1) ...
Setting up libkrb5-3:armhf (1.14.2+dfsg-1) ...
Setting up libpoppler61:armhf (0.44.0-3) ...
Setting up libx11-dev:armhf (2:1.6.3-1) ...
Setting up libxft2:armhf (2.3.2-1) ...
Setting up fontconfig (2.11.0-6.4) ...
Regenerating fonts cache... done.
Setting up libfontconfig1-dev:armhf (2.11.0-6.4) ...
Setting up libsm-dev:armhf (2:1.2.2-1+b1) ...
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up po-debconf (1.0.19) ...
Setting up libxcb-shm0-dev:armhf (1.11.1-1) ...
Setting up libxrender-dev:armhf (1:0.9.9-2) ...
Setting up libmagickcore-6.q16-2:armhf (8:6.8.9.9-7.2) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libgssapi-krb5-2:armhf (1.14.2+dfsg-1) ...
Setting up libxcb-render0-dev:armhf (1.11.1-1) ...
Setting up fonts-sil-gentiumplus-compact (5.000-2) ...
Setting up libxft-dev (2.3.2-1) ...
Setting up libxext-dev:armhf (2:1.3.3-1) ...
Setting up libpango-1.0-0:armhf (1.40.1-1) ...
Setting up fonts-sil-gentiumplus (5.000-1) ...
Setting up libcups2:armhf (2.1.4-4) ...
Setting up libxi6:armhf (2:1.7.6-1) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up libcairo2:armhf (1.14.6-1+b1) ...
Setting up libcairo-script-interpreter2:armhf (1.14.6-1+b1) ...
Setting up libcairo-gobject2:armhf (1.14.6-1+b1) ...
Setting up libmagickwand-6.q16-2:armhf (8:6.8.9.9-7.2) ...
Setting up libpangoft2-1.0-0:armhf (1.40.1-1) ...
Setting up gir1.2-freedesktop:armhf (1.48.0-3) ...
Setting up libpangoxft-1.0-0:armhf (1.40.1-1) ...
Setting up imagemagick-6.q16 (8:6.8.9.9-7.2) ...
Setting up libpangocairo-1.0-0:armhf (1.40.1-1) ...
Setting up gir1.2-pango-1.0:armhf (1.40.1-1) ...
Setting up imagemagick (8:6.8.9.9-7.2) ...
update-alternatives: using /usr/bin/compare-im6 to provide /usr/bin/compare (compare) in auto mode
update-alternatives: using /usr/bin/animate-im6 to provide /usr/bin/animate (animate) in auto mode
update-alternatives: using /usr/bin/convert-im6 to provide /usr/bin/convert (convert) in auto mode
update-alternatives: using /usr/bin/composite-im6 to provide /usr/bin/composite (composite) in auto mode
update-alternatives: using /usr/bin/conjure-im6 to provide /usr/bin/conjure (conjure) in auto mode
update-alternatives: using /usr/bin/import-im6 to provide /usr/bin/import (import) in auto mode
update-alternatives: using /usr/bin/identify-im6 to provide /usr/bin/identify (identify) in auto mode
update-alternatives: using /usr/bin/stream-im6 to provide /usr/bin/stream (stream) in auto mode
update-alternatives: using /usr/bin/display-im6 to provide /usr/bin/display (display) in auto mode
update-alternatives: using /usr/bin/montage-im6 to provide /usr/bin/montage (montage) in auto mode
update-alternatives: using /usr/bin/mogrify-im6 to provide /usr/bin/mogrify (mogrify) in auto mode
Setting up python3 (3.5.1-4) ...
Setting up ruby2.3 (2.3.1-2) ...
Setting up libglib2.0-dev (2.48.1-2) ...
Setting up libcupsfilters1:armhf (1.10.0-1) ...
Setting up libcupsimage2:armhf (2.1.4-4) ...
Setting up dh-strip-nondeterminism (0.019-1) ...
Setting up ruby (1:2.3.0+4) ...
Setting up libgs9 (9.19~dfsg-1+b1) ...
Setting up libharfbuzz-dev:armhf (1.2.7-1) ...
Setting up dh-python (2.20160721) ...
Setting up debhelper (9.20160709) ...
Setting up dh-autoreconf (12) ...
Setting up libcairo2-dev (1.14.6-1+b1) ...
Setting up rake (10.5.0-2) ...
Setting up texlive-binaries (2016.20160513.41080-4) ...
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 libpango1.0-dev (1.40.1-1) ...
Setting up libruby2.3:armhf (2.3.1-2) ...
Processing triggers for tex-common (6.05) ...
update-language: texlive-base not installed and configured, doing nothing!
texlive-base is not ready, skipping fmtutil --all call
Setting up texlive-base (2016.20160623-1) ...
/usr/bin/tl-paper: setting paper size for dvips to a4.
/usr/bin/tl-paper: setting paper size for dvipdfmx to a4.
/usr/bin/tl-paper: setting paper size for xdvi to a4.
/usr/bin/tl-paper: setting paper size for pdftex to a4.
Processing triggers for tex-common (6.05) ...
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.
Setting up texlive-latex-base (2016.20160623-1) ...
Setting up texlive-fonts-extra (2016.20160623-1) ...
Setting up texlive-fonts-recommended (2016.20160623-1) ...
Processing triggers for tex-common (6.05) ...
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.
Setting up texlive-latex-recommended (2016.20160623-1) ...
Setting up texlive-pictures (2016.20160623-1) ...
Processing triggers for tex-common (6.05) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-latex-extra (2016.20160623-1) ...
Processing triggers for tex-common (6.05) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up sbuild-build-depends-genometools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.23-1+rpi1) ...
Processing triggers for systemd (230-5) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.7 g++-5_5.4.0-4 gcc-5_5.4.0-4 libc6-dev_2.23-1+rpi1 libstdc++-5-dev_5.4.0-4 libstdc++6_6.1.1-1+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre2 asciidoc_8.6.9-3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-5 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 console-setup_1.146 console-setup-linux_1.146 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-3 cpp-5_5.4.0-4 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160709 debianutils_4.8 dh-autoreconf_12 dh-python_2.20160721 dh-strip-nondeterminism_0.019-1 diffutils_1:3.3-3 dmsetup_2:1.02.127-1 docbook-xsl_1.79.1+dfsg-1 dpkg_1.18.7 dpkg-dev_1.18.7 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 faketime_0.9.6-7 file_1:5.28-2 findutils_4.6.0+git+20160517-5 fontconfig_2.11.0-6.4 fontconfig-config_2.11.0-6.4 fonts-cabin_1.5-2 fonts-comfortaa_2.003-1 fonts-crosextra-caladea_20130214-1 fonts-crosextra-carlito_20130920-1 fonts-dejavu-core_2.36-1 fonts-dejavu-extra_2.36-1 fonts-ebgaramond_0.015+git20130628-3 fonts-ebgaramond-extra_0.015+git20130628-3 fonts-font-awesome_4.6.3~dfsg-1 fonts-freefont-otf_20120503-4 fonts-freefont-ttf_20120503-4 fonts-gfs-artemisia_1.1-5 fonts-gfs-complutum_1.1-6 fonts-gfs-didot_1.1-6 fonts-gfs-neohellenic_1.1-6 fonts-gfs-olga_1.1-5 fonts-gfs-solomos_1.1-5 fonts-junicode_0.7.8-2 fonts-lato_2.0-1 fonts-linuxlibertine_5.3.0-2 fonts-lobster_2.0-2 fonts-lobstertwo_2.0-2 fonts-oflb-asana-math_000.907-6 fonts-roboto-hinted_2:0~20160106-1 fonts-sil-gentium_20081126:1.03-1 fonts-sil-gentium-basic_1.1-7 fonts-sil-gentiumplus_5.000-1 fonts-sil-gentiumplus-compact_5.000-2 fonts-stix_1.1.1-4 fuse2fs_1.43.1-1 g++_4:5.3.1-3 g++-5_5.4.0-4 gcc_4:5.3.1-3 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5_5.4.0-4 gcc-5-base_5.4.0-4 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gir1.2-freedesktop_1.48.0-3 gir1.2-glib-2.0_1.48.0-3 gir1.2-pango-1.0_1.40.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hicolor-icon-theme_0.15-1 hostname_3.18 icu-devtools_55.1-7 ifupdown_0.8.13 imagemagick_8:6.8.9.9-7.2 imagemagick-6.q16_8:6.8.9.9-7.2 imagemagick-common_8:6.8.9.9-7.2 init_1.36 init-system-helpers_1.36 initscripts_2.88dsf-59.7 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 iproute2_4.3.0-1 kbd_2.0.3-2 keyboard-configuration_1.146 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3~pre2 libarchive-zip-perl_1.57-1 libasan2_5.4.0-4 libatm1_1:2.5.1-1.6 libatomic1_6.1.1-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.5.2-1+rpi1 libaudit1_1:2.5.2-1+rpi1 libavahi-client3_0.6.32-1 libavahi-common-data_0.6.32-1 libavahi-common3_0.6.32-1 libbam-dev_0.1.19-2 libblkid1_2.28-5 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.23-1+rpi1 libc-dev-bin_2.23-1+rpi1 libc6_2.23-1+rpi1 libc6-dev_2.23-1+rpi1 libcairo-gobject2_1.14.6-1+b1 libcairo-script-interpreter2_1.14.6-1+b1 libcairo2_1.14.6-1+b1 libcairo2-dev_1.14.6-1+b1 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-1+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libcups2_2.1.4-4 libcupsfilters1_1.10.0-1 libcupsimage2_2.1.4-4 libdatrie1_0.2.10-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.213 libdevmapper1.02.1_2:1.02.127-1 libdpkg-perl_1.18.7 libdrm2_2.4.68-1 libelf1_0.166-2 libexpat1_2.2.0-1 libexpat1-dev_2.2.0-1 libfakeroot_1.21-1 libfaketime_0.9.6-7 libfdisk1_2.28-5 libffi6_3.2.1-4 libfftw3-double3_3.3.4-2+rvt+b1 libfile-stripnondeterminism-perl_0.019-1 libfontconfig1_2.11.0-6.4 libfontconfig1-dev_2.11.0-6.4 libfreetype6_2.6.3-3+b1 libfreetype6-dev_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-5-dev_5.4.0-4 libgcc1_1:6.1.1-1+rpi1 libgcrypt20_1.7.1-2 libgdbm3_1.8.3-14 libgirepository-1.0-1_1.48.0-3 libglib2.0-0_2.48.1-2 libglib2.0-bin_2.48.1-2 libglib2.0-data_2.48.1-2 libglib2.0-dev_2.48.1-2 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.4.14-1 libgomp1_6.1.1-1+rpi1 libgpg-error0_1.23-1 libgraphite2-3_1.3.8-1 libgraphite2-dev_1.3.8-1 libgs9_9.19~dfsg-1+b1 libgs9-common_9.19~dfsg-1 libgssapi-krb5-2_1.14.2+dfsg-1 libharfbuzz-dev_1.2.7-1 libharfbuzz-gobject0_1.2.7-1 libharfbuzz-icu0_1.2.7-1 libharfbuzz0b_1.2.7-1 libhogweed4_3.2-1 libice-dev_2:1.0.9-1+b1 libice6_2:1.0.9-1+b1 libicu-dev_55.1-7 libicu55_55.1-7 libidn11_1.32-3.1 libijs-0.35_0.35-12 libisl15_0.17.1-1 libjbig0_2.1-3.1 libjbig2dec0_0.13-2 libjpeg62-turbo_1:1.5.0-1 libk5crypto3_1.14.2+dfsg-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkpathsea6_2016.20160513.41080-4 libkrb5-3_1.14.2+dfsg-1 libkrb5support0_1.14.2+dfsg-1 liblcms2-2_2.7-1 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 liblocale-gettext-perl_1.07-3 liblqr-1-0_0.4.2-2 libltdl7_2.4.6-0.1 liblua5.1-0_5.1.5-8 liblua5.1-0-dev_5.1.5-8 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 liblzo2-2_2.08-1.2 libmagic1_1:5.28-2 libmagickcore-6.q16-2_8:6.8.9.9-7.2 libmagickwand-6.q16-2_8:6.8.9.9-7.2 libmount1_2.28-5 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libnettle6_3.2-1 libnspr4_2:4.12-2 libnss3_2:3.23-2 libopenjp2-7_2.1.1-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpango-1.0-0_1.40.1-1 libpango1.0-dev_1.40.1-1 libpangocairo-1.0-0_1.40.1-1 libpangoft2-1.0-0_1.40.1-1 libpangoxft-1.0-0_1.40.1-1 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre16-3_2:8.38-3.1 libpcre3_2:8.38-3.1 libpcre3-dev_2:8.38-3.1 libpcre32-3_2:8.38-3.1 libpcrecpp0v5_2:8.38-3.1 libperl5.22_5.22.2-2 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpixman-1-dev_0.33.6-1 libplymouth4_0.9.2-3 libpng-dev_1.6.23-1 libpng12-0_1.2.54-6 libpng16-16_1.6.23-1 libpoppler61_0.44.0-3 libpotrace0_1.13-2 libprocps5_2:3.3.11-3 libptexenc1_2016.20160513.41080-4 libpthread-stubs0-dev_0.3-4 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-1 libpython2.7-stdlib_2.7.12-1 libpython3-stdlib_3.5.1-4 libpython3.5-minimal_3.5.2-2 libpython3.5-stdlib_3.5.2-2 libreadline-dev_6.3-8+b3 libreadline6_6.3-8+b3 libreadline6-dev_6.3-8+b3 libruby2.3_2.3.1-2 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm-dev_2:1.2.2-1+b1 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28-5 libsqlite3-0_3.13.0-1 libsqlite3-dev_3.13.0-1 libss2_1.43.1-1 libssl1.0.2_1.0.2h-1 libstdc++-5-dev_5.4.0-4 libstdc++6_6.1.1-1+rpi1 libsynctex1_2016.20160513.41080-4 libsystemd0_230-5 libtasn1-6_4.8-1 libtexlua52_2016.20160513.41080-4 libtexluajit2_2016.20160513.41080-4 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.25-1 libthai0_0.1.25-1 libtiff5_4.0.6-2 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160625-1 libtinfo5_6.0+20160625-1 libtool_2.4.6-0.1 libtre-dev_0.8.0-4 libtre5_0.8.0-4 libubsan0_6.1.1-1+rpi1 libudev1_230-5 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libx11-dev_2:1.6.3-1 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.11.1-1 libxcb-render0-dev_1.11.1-1 libxcb-shm0_1.11.1-1 libxcb-shm0-dev_1.11.1-1 libxcb1_1.11.1-1 libxcb1-dev_1.11.1-1 libxdmcp-dev_1:1.1.2-1.1 libxdmcp6_1:1.1.2-1.1 libxext-dev_2:1.3.3-1 libxext6_2:1.3.3-1 libxft-dev_2.3.2-1 libxft2_2.3.2-1 libxi6_2:1.7.6-1 libxml2_2.9.4+dfsg1-1 libxml2-utils_2.9.4+dfsg1-1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.11-1+b1 libxrender-dev_1:0.9.9-2 libxrender1_1:0.9.9-2 libxslt1.1_1.1.28-4 libxt6_1:1.1.5-1 libyaml-0-2_0.1.6-3 libzzip-0-13_0.13.62-3 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 lua-filesystem_1.6.3-1 lua-filesystem-dev_1.6.3-1 lua-lpeg_0.12.2-1 lua-lpeg-dev_0.12.2-1 lua-md5_1.2+git+1+8d87fee-1 lua-md5-dev_1.2+git+1+8d87fee-1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.06-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-5 multiarch-support_2.23-1+rpi1 ncurses-base_6.0+20160319-2 ncurses-bin_6.0+20160319-2 netbase_5.3 openssl_1.0.2h-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-2 perl-base_5.22.2-2 perl-modules-5.22_5.22.2-2 pkg-config_0.29-4 po-debconf_1.0.19 poppler-data_0.4.7-7 preview-latex-style_11.87-3+deb8u1 procps_2:3.3.11-3 psmisc_22.21-2.1 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-1 python2.7-minimal_2.7.12-1 python3_3.5.1-4 python3-minimal_3.5.1-4 python3.5_3.5.2-2 python3.5-minimal_3.5.2-2 rake_10.5.0-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 ruby_1:2.3.0+4 ruby-did-you-mean_1.0.0-2 ruby-minitest_5.9.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.3.0-1 ruby-test-unit_3.1.7-2 ruby2.3_2.3.1-2 rubygems-integration_1.10 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-genometools-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 sgml-base_1.28 startpar_0.59-3 systemd_230-5 systemd-sysv_230-5 sysv-rc_2.88dsf-59.7 sysvinit-utils_2.88dsf-59.7 t1utils_1.39-2 tar_1.29-1+rpi1 tex-common_6.05 texlive-base_2016.20160623-1 texlive-binaries_2016.20160513.41080-4 texlive-fonts-extra_2016.20160623-1 texlive-fonts-recommended_2016.20160623-1 texlive-latex-base_2016.20160623-1 texlive-latex-extra_2016.20160623-1 texlive-latex-recommended_2016.20160623-1 texlive-pictures_2016.20160623-1 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 ttf-adf-universalis_0.20090423-2 tzdata_2016f-1 ucf_3.0036 udev_230-5 util-linux_2.28-5 x11-common_1:7.7+16 x11proto-core-dev_7.0.29-1 x11proto-input-dev_2.3.2-1 x11proto-kb-dev_1.0.7-1 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.3.0-1 xdg-utils_1.1.1-1 xkb-data_2.17-1 xml-core_0.13+nmu2 xorg-sgml-doctools_1:1.11-1 xsltproc_1.1.28-4 xtrans-dev_1.3.5-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1

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


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

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Jul 23 11:15:41 2016 UTC using RSA key ID F09F4872
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./genometools_1.5.9+ds-2.dsc
dpkg-source: info: extracting genometools in genometools-1.5.9+ds
dpkg-source: info: unpacking genometools_1.5.9+ds.orig.tar.xz
dpkg-source: info: unpacking genometools_1.5.9+ds-2.debian.tar.xz
dpkg-source: info: applying remove_png_timestamps
dpkg-source: info: applying use-pkgconfig
dpkg-source: info: applying adding_soname
dpkg-source: info: applying libbam-fix
dpkg-source: info: applying remove-gitignores
dpkg-source: info: applying fix-exports
dpkg-source: info: applying split-manuals
dpkg-source: info: applying use-mx32
dpkg-source: info: applying gtdoc-traverse-sorted
dpkg-source: info: applying ignore-m32-m64.patch

Check disc space
----------------

Sufficient free space for build

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

DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-8fbd04cf-b271-46f5-8386-9ac41699de58
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: info: source package genometools
dpkg-buildpackage: info: source version 1.5.9+ds-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build genometools-1.5.9+ds
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --with python2
   dh_testdir
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
mkdir obj
/usr/bin/make cleanup
make[2]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
rm -rf lib
find obj -name '*.o' -delete
rm -f obj/amalgamation.c
rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests
/usr/bin/make -s -C /<<BUILDDIR>>/genometools-1.5.9+ds/doc/devguide clean
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/devguide'
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/devguide'
/usr/bin/make -s -C /<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals clean
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals'
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals'
rm -f doc/manuals/api_reference.tex \
          doc/manuals/gtscript_reference.tex
find doc . -name "*.toc" -delete
rm -f www/genometools.org/htdocs/images/callbacks.png \
          www/genometools.org/htdocs/images/parsed.png    \
          www/genometools.org/htdocs/images/constructed.png \
          doc/manuals/annotationsketch.pdf
rm -f www/genometools.org/htdocs/examples.html
rm -rf doc/manpages
find testdata \( -name '*.esq' -o -name '*.sds' -o -name '*.ssp' \
	 -o -name '*.ois' -o -name '*.al1' \)  \
   -a ! \( -name 'foo.[36][24].*' \) -delete
find obj -name '*.splint' -delete
find obj -name '*.check' -delete
find obj -name '*.sb' -delete
rm -rf bin obj
rm -rf gtpython/build
/usr/bin/make -s -C /<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals cleanup
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals'
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals'
make[2]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
cd doc/manuals; /usr/bin/make cleanup
make[2]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals'
rm -f *.aux  *.log *.bbl  *.blg *.dvi *.mer *.mct *.mbd comment.cut
rm -f *.out *.toc
rm -f U89959.fna read[12].fna 
rm -f reads.al1 reads.esq reads.lcp reads.llv reads.prj reads.suf
rm -f tallymer-tmp.tex
rm -f tagerator-tmp.tex Q1.gz pck-human.*
rm -f readjoiner.pdf hop.pdf ltrharvest.pdf ltrdigest.pdf uniquesub.pdf matstat.pdf mgth.pdf packedindex.pdf repfind.pdf tallymer.pdf tagerator.pdf genomediff.pdf
make[2]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals'
# should be deleted inside doc/manuals/Makefile
rm -f doc/manuals/annotationsketch.out \
      doc/manuals/api_reference.tex    \
      doc/manuals/gtscript_reference.tex
find doc . -name "*.toc" -delete
find testdata \( -name '*.ois' -or -name '*.sds' -or -name '*.esq' -or \
      -name '*.ssp' -or -name '*.des' -or -name "*.md5"  \) -and \( -not \
      -name '*foo.32.*' -not -name '*foo.64.*' \) -delete
rm -f www/genometools.org/htdocs/images/callbacks.png \
      www/genometools.org/htdocs/images/parsed.png    \
      www/genometools.org/htdocs/images/constructed.png \
      doc/manuals/annotationsketch.pdf
rm -f www/genometools.org/htdocs/examples.html \
      www/genometools.org/htdocs/libgenometools.html
rm -rf gtpython/build
rm -rf obj
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
   dh_clean
 debian/rules build-arch
dh build-arch --with python2
   dh_testdir -a
   dh_update_autotools_config -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
faketime -f "`TZ=UTC date -d @1469271266 +'%Y-%m-%d %H:%M:%S'`" dh_auto_build -- useshared=yes x32=no 64bit=no errorcheck=no all docs manuals
	make -j1 useshared=yes x32=no 64bit=no errorcheck=no all docs manuals
make[2]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
[create obj/gt_config.h]
[compile alphabet.o]
[compile array.o]
[compile array2dim.o]
[compile array2dim_sparse.o]
[compile array3dim.o]
[compile basename.o]
[compile bioseq.o]
[compile bioseq_col.o]
[compile bioseq_iterator.o]
[compile bitbuffer.o]
[compile bitpackstringop.o]
[compile bitpackstringop16.o]
[compile bitpackstringop32.o]
[compile bitpackstringop64.o]
[compile bitpackstringop8.o]
[compile bittab.o]
[compile bool_matrix.o]
[compile bsearch.o]
[compile byte_popcount.o]
[compile byte_select.o]
[compile checkbitpackarray.o]
[compile checkbitpackstring-int.o]
[compile checkbitpackstring.o]
[compile checkbitpackstring16.o]
[compile checkbitpackstring32.o]
[compile checkbitpackstring64.o]
[compile checkbitpackstring8.o]
[compile class_alloc.o]
[compile class_alloc_lock.o]
[compile codon_iterator.o]
[compile codon_iterator_encseq.o]
[compile codon_iterator_simple.o]
[compile colorspace.o]
[compile combinatorics.o]
[compile compact_ulong_store.o]
[compile compat.o]
[compile complement.o]
[compile countingsort.o]
[compile cstr.o]
[compile cstr_array.o]
[compile cstr_table.o]
[compile desc_buffer.o]
[compile disc_distri.o]
[compile dlist.o]
[compile dual-pivot-qsort.o]
[compile dyn_bittab.o]
[compile dynalloc.o]
[compile eansi.o]
[compile ebzlib.o]
[compile encseq.o]
[compile encseq_access_type.o]
[compile encseq_col.o]
[compile encseq_metadata.o]
[compile encseq_options.o]
[compile encseq_ptr.o]
[compile endianess.o]
[compile error.o]
[compile example.o]
[compile example_a.o]
[compile example_b.o]
[compile ezlib.o]
[compile fa.o]
[compile fasta.o]
[compile fasta_reader.o]
[compile fasta_reader_fsm.o]
[compile fasta_reader_rec.o]
[compile fasta_reader_seqit.o]
[compile fastq.o]
[compile file.o]
[compile fileutils.o]
[compile gc_content.o]
[compile grep.o]
[compile gtdatapath.o]
[compile hashmap.o]
[compile hashtable.o]
[compile init.o]
[compile interval_tree.o]
[compile io.o]
[compile log.o]
[compile logger.o]
[compile ma.o]
[compile mapspec.o]
[compile mathsupport.o]
[compile md5_encoder.o]
[compile md5_fingerprint.o]
[compile md5_seqid.o]
[compile md5_tab.o]
[compile msort.o]
[compile multithread.o]
[compile option.o]
[compile orf.o]
[compile output_file.o]
[compile parseutils.o]
[compile password_entry.o]
[compile phase.o]
[compile process.o]
[compile progressbar.o]
[compile qsort-ulong.o]
[compile qsort_r.o]
[compile quality.o]
[compile queue.o]
[compile radix_sort.o]
[compile range.o]
[compile readmode.o]
[compile safearith.o]
[compile score_function.o]
[compile score_matrix.o]
[compile seq.o]
[compile seq_col.o]
[compile seq_info_cache.o]
[compile seq_iterator.o]
[compile seq_iterator_fastq.o]
[compile seq_iterator_sequence_buffer.o]
[compile sequence_buffer.o]
[compile sequence_buffer_embl.o]
[compile sequence_buffer_fasta.o]
[compile sequence_buffer_fastq.o]
[compile sequence_buffer_gb.o]
[compile sequence_buffer_plain.o]
[compile showtime.o]
[compile sig.o]
[compile spacepeak.o]
[compile splitter.o]
[compile str.o]
[compile str_array.o]
[compile str_cache.o]
[compile strand.o]
[compile strcmp.o]
[compile string_distri.o]
[compile symbol.o]
[compile thread.o]
[compile timer.o]
[compile tokenizer.o]
[compile tool.o]
[compile tool_iterator.o]
[compile toolbox.o]
[compile tooldriver.o]
[compile trans_table.o]
[compile translator.o]
[compile unit_testing.o]
[compile version.o]
[compile versionfunc.o]
[compile warning.o]
[compile xansi.o]
[compile xbsd.o]
[compile xbzlib.o]
[compile xposix.o]
[compile xzlib.o]
[compile yarandom.o]
[compile add_ids_stream.o]
[compile add_ids_visitor.o]
[compile add_introns_stream.o]
[compile affinealign.o]
[compile aligned_segment.o]
[compile aligned_segments_pile.o]
[compile alignment.o]
[compile anno_db_gfflike.o]
[compile anno_db_schema.o]
[compile array_in_stream.o]
[compile array_out_stream.o]
[compile assembly_stats_calculator.o]
[compile bed_in_stream.o]
[compile bed_parser.o]
[compile bitinstream.o]
[compile bitoutstream.o]
[compile blast_process_call.o]
[compile buffer_stream.o]
[compile cds_check_stream.o]
[compile cds_check_visitor.o]
[compile cds_stream.o]
[compile cds_visitor.o]
[compile chain.o]
[compile check_boundaries_visitor.o]
[compile chseqids_stream.o]
[compile clustered_set.o]
[compile clustered_set_uf.o]
[compile coin_hmm.o]
[compile collect_ids_visitor.o]
[compile comment_node.o]
[compile compressed_bitsequence.o]
[compile condenseq.o]
[compile condenseq_creator.o]
[compile condenseq_search_arguments.o]
[compile consensus_sa.o]
[compile csa_gene.o]
[compile csa_splice_form.o]
[compile csa_stream.o]
[compile csa_variable_strands.o]
[compile csa_visitor.o]
[compile cstr_iterator.o]
[compile diagonalbandalign.o]
[compile diagonalbandalign_affinegapcost.o]
[compile dice_hmm.o]
[compile dot_out_stream.o]
[compile dot_visitor.o]
[compile dup_feature_stream.o]
[compile dup_feature_visitor.o]
[compile editscript.o]
[compile elias_gamma.o]
[compile encdesc.o]
[compile encdesc_header_io.o]
[compile eof_node.o]
[compile evaluator.o]
[compile extract_feature_sequence.o]
[compile extract_feature_stream.o]
[compile extract_feature_visitor.o]
[compile fasta_header_iterator.o]
[compile feature_in_stream.o]
[compile feature_index.o]
[compile feature_index_memory.o]
[compile feature_info.o]
[compile feature_node.o]
[compile feature_node_iterator.o]
[compile feature_node_observer.o]
[compile feature_out_stream.o]
[compile feature_stream.o]
[compile feature_visitor.o]
[compile gap_str.o]
[compile genome_node.o]
[compile gff3_escaping.o]
[compile gff3_in_stream.o]
[compile gff3_in_stream_plain.o]
[compile gff3_linesorted_out_stream.o]
[compile gff3_numsorted_out_stream.o]
[compile gff3_out_stream.o]
[compile gff3_output.o]
[compile gff3_parser.o]
[compile gff3_visitor.o]
[compile globalchaining.o]
[compile golomb.o]
[compile gtdatahelp.o]
[compile gtf_in_stream.o]
[compile gtf_out_stream.o]
[compile gtf_parser.o]
[compile gtf_visitor.o]
[compile hcr.o]
[compile hmm.o]
[compile hpol_processor.o]
[compile huffcode.o]
[compile id_to_md5_stream.o]
[compile id_to_md5_visitor.o]
[compile inter_feature_stream.o]
[compile inter_feature_visitor.o]
[compile intset.o]
[compile intset_16.o]
[compile intset_32.o]
[compile intset_8.o]
[compile intset_combined.o]
[compile io_function_pointers.o]
[compile kmer_database.o]
[compile linearalign.o]
[compile linearalign_affinegapcost.o]
[compile linspace_management.o]
[compile load_stream.o]
[compile luahelper.o]
[compile luaserialize.o]
[compile mapping.o]
[compile match.o]
[compile match_blast.o]
[compile match_iterator.o]
[compile match_iterator_blast.o]
[compile match_iterator_last.o]
[compile match_iterator_open.o]
[compile match_iterator_sw.o]
[compile match_last.o]
[compile match_open.o]
[compile match_sw.o]
[compile match_visitor.o]
[compile maxcoordvalue.o]
[compile md5_to_id_stream.o]
[compile md5_to_id_visitor.o]
[compile md5set.o]
[compile merge_feature_stream.o]
[compile merge_feature_visitor.o]
[compile merge_stream.o]
[compile meta_node.o]
[compile multi_sanitizer_visitor.o]
[compile multieoplist.o]
[compile mutate.o]
[compile node_stream.o]
[compile node_visitor.o]
[compile obo_parse_tree.o]
[compile obo_stanza.o]
[compile orf_finder_stream.o]
[compile orf_finder_visitor.o]
[compile orf_iterator.o]
[compile orphanage.o]
[compile permute_words.o]
[compile popcount_tab.o]
[compile priority_queue.o]
[compile ranked_list.o]
[compile rbtree.o]
[compile rcr.o]
[compile rdb.o]
[compile rdb_sqlite.o]
[compile rdb_visitor.o]
[compile reconstructalignment.o]
[compile region_mapping.o]
[compile region_node.o]
[compile region_node_builder.o]
[compile regioncov_visitor.o]
[compile regular_seqid.o]
[compile reverse.o]
[compile rmq.o]
[compile safe_popen.o]
[compile sam_alignment.o]
[compile sam_query_name_iterator.o]
[compile samfile_encseq_mapping.o]
[compile samfile_iterator.o]
[compile sampling.o]
[compile scorehandler.o]
[compile script_filter.o]
[compile script_wrapper_stream.o]
[compile script_wrapper_visitor.o]
[compile select_stream.o]
[compile select_visitor.o]
[compile seqid2file.o]
[compile seqid2seqnum_mapping.o]
[compile seqpos_classifier.o]
[compile sequence_node.o]
[compile sequence_node_add_stream.o]
[compile sequence_node_out_stream.o]
[compile sequence_node_out_visitor.o]
[compile set_source_visitor.o]
[compile shredder.o]
[compile snp_annotator_stream.o]
[compile snp_annotator_visitor.o]
[compile sort_stream.o]
[compile spec_results.o]
[compile spec_visitor.o]
[compile splice_site_info_stream.o]
[compile splice_site_info_visitor.o]
[compile splicedseq.o]
[compile squarealign.o]
[compile sspliced_alignment.o]
[compile sspliced_alignment_parsing.o]
[compile stat_stream.o]
[compile stat_visitor.o]
[compile stream_evaluator.o]
[compile string_matching.o]
[compile swalign.o]
[compile tag_value_map.o]
[compile targetbest_select_stream.o]
[compile tidy_region_node_stream.o]
[compile tidy_region_node_visitor.o]
[compile tir_stream.o]
[compile transcript_bittabs.o]
[compile transcript_counts.o]
[compile transcript_evaluators.o]
[compile transcript_exons.o]
[compile transcript_used_exons.o]
[compile type_checker.o]
[compile type_checker_builtin.o]
[compile type_checker_obo.o]
[compile type_graph.o]
[compile type_node.o]
[compile typecheck_info.o]
[compile uint64hashtable.o]
[compile union_find.o]
[compile uniq_stream.o]
[compile visitor_stream.o]
[compile wtree.o]
[compile wtree_encseq.o]
[compile xrf_abbr_entry.o]
[compile xrf_abbr_parse_tree.o]
[compile xrf_checker.o]
[compile xrfcheck_info.o]
[compile alphabet_lua.o]
[compile annotationsketch_lua.o]
[compile bittab_lua.o]
[compile canvas_lua.o]
[compile cds_stream_lua.o]
[compile csa_stream_lua.o]
[compile diagram_lua.o]
[compile encseq_lua.o]
[compile feature_index_lua.o]
[compile feature_node_iterator_lua.o]
[compile feature_stream_lua.o]
[compile feature_visitor_lua.o]
[compile genome_node_lua.o]
[compile genome_stream_lua.o]
[compile genome_visitor_lua.o]
[compile gt_lua.o]
[compile gtcore_lua.o]
[compile gtext_lua.o]
[compile image_info_lua.o]
[compile layout_lua.o]
[compile mathsupport_lua.o]
[compile range_lua.o]
[compile region_mapping_lua.o]
[compile score_matrix_lua.o]
[compile stream_evaluator_lua.o]
[compile translate_lua.o]
[compile apmeoveridx.o]
[compile asqg_writer.o]
[compile bare-encseq.o]
[compile bcktab.o]
[compile cgr_spacedseed.o]
[compile chain2dim.o]
[compile chainofin.o]
[compile cutendpfx.o]
[compile diagbandseed.o]
[compile dist-short.o]
[compile echoseq.o]
[compile eis-blockcomp-param.o]
[compile eis-blockcomp.o]
[compile eis-bwtseq-construct.o]
[compile eis-bwtseq-context-param.o]
[compile eis-bwtseq-context.o]
[compile eis-bwtseq-extinfo.o]
[compile eis-bwtseq-param.o]
[compile eis-bwtseq-sass.o]
[compile eis-bwtseq.o]
[compile eis-encidxseq-construct.o]
[compile eis-encidxseq-param.o]
[compile eis-encidxseq.o]
[compile eis-mrangealphabet.o]
[compile eis-sa-common.o]
[compile eis-seqblocktranslate.o]
[compile eis-seqranges.o]
[compile eis-sequencemultiread.o]
[compile eis-specialsrank.o]
[compile eis-suffixarray-interface.o]
[compile eis-suffixerator-interface.o]
[compile eis-voiditf.o]
[compile encseq2offset.o]
[compile enum-patt.o]
[compile esa-bottomup.o]
[compile esa-dfs.o]
[compile esa-lcpintervals.o]
[compile esa-map.o]
[compile esa-maxpairs.o]
[compile esa-merge.o]
[compile esa-minunique.o]
[compile esa-mmsearch.o]
[compile esa-scanprj.o]
[compile esa-seqread.o]
[compile esa-shulen.o]
[compile esa-splititv-simple.o]
[compile esa-splititv.o]
[compile esa-spmitvs.o]
[compile esa-spmsk.o]
[compile esa_lcpintervals_visitor.o]
[compile esa_spmitvs_visitor.o]
[compile esa_visitor.o]
[compile firstcodes-accum.o]
[compile firstcodes-cache.o]
[compile firstcodes-insert.o]
[compile firstcodes-psbuf.o]
[compile firstcodes-scan.o]
[compile firstcodes-spacelog.o]
[compile firstcodes-tab.o]
[compile firstcodes.o]
[compile fmi-fwduni.o]
[compile fmi-keyval.o]
[compile fmi-locate.o]
[compile fmi-map.o]
[compile fmi-mapspec.o]
[compile fmi-mkindex.o]
[compile fmi-save.o]
[compile fmi-sufbwtstream.o]
[compile ft-front-generation.o]
[compile ft-front-prune.o]
[compile ft-polish.o]
[compile ft-trimstat.o]
[compile giextract.o]
[compile greedyedist.o]
[compile greedyfwdmat.o]
[compile hashfirstcodes.o]
[compile hlk-version.o]
[compile hplstore.o]
[compile idx-limdfs.o]
[compile idxlocali.o]
[compile idxlocalidp.o]
[compile idxlocalisw.o]
[compile index_options.o]
[compile initbasepower.o]
[compile initeqsvec.o]
[compile iter-window.o]
[compile kmer2string.o]
[compile lua_tools.o]
[compile marksubstring.o]
[compile merger-trie.o]
[compile mssufpat.o]
[compile myersapm.o]
[compile nullcols.o]
[compile optionargmode.o]
[compile pck-count-nodes.o]
[compile pckbucket.o]
[compile pckdfs.o]
[compile prsqualint.o]
[compile pssm.o]
[compile querymatch-align.o]
[compile querymatch.o]
[compile radixsort_str.o]
[compile randomcodes-correct.o]
[compile randomcodes-find-seldom.o]
[compile randomcodes-hpcorrect.o]
[compile randomcodes-insert.o]
[compile randomcodes-sfx-partssuf.o]
[compile randomcodes-tab.o]
[compile randomcodes.o]
[compile rdj-cntlist.o]
[compile rdj-contfind-bottomup.o]
[compile rdj-contfinder.o]
[compile rdj-contigpaths.o]
[compile rdj-contigs-graph.o]
[compile rdj-contigs-writer.o]
[compile rdj-errfind.o]
[compile rdj-ovlfind-bf.o]
[compile rdj-ovlfind-dp.o]
[compile rdj-ovlfind-gusfield.o]
[compile rdj-ovlfind-kmp.o]
[compile rdj-pairwise.o]
[compile rdj-spmfind.o]
[compile rdj-spmlist.o]
[compile rdj-spmproc.o]
[compile rdj-strgraph.o]
[compile rdj-twobitenc-editor.o]
[compile rdj-version.o]
[compile reads2twobit.o]
[compile reads_libraries_table.o]
[compile revcompl.o]
[compile seed-extend-iter.o]
[compile seed-extend.o]
[compile seqabstract.o]
[compile seqnumrelpos.o]
[compile sfx-apfxlen.o]
[compile sfx-bentsedg.o]
[compile sfx-bltrie.o]
[compile sfx-copysort.o]
[compile sfx-diffcov.o]
[compile sfx-enumcodes.o]
[compile sfx-lcpvalues.o]
[compile sfx-linlcp.o]
[compile sfx-lwcheck.o]
[compile sfx-mappedstr.o]
[compile sfx-maprange.o]
[compile sfx-opt.o]
[compile sfx-outprj.o]
[compile sfx-partssuf.o]
[compile sfx-radixsort.o]
[compile sfx-run.o]
[compile sfx-sain.o]
[compile sfx-shortreadsort.o]
[compile sfx-suffixer.o]
[compile sfx-suffixgetset.o]
[compile sfx-suftaborder.o]
[compile shu-dfs.o]
[compile shu-divergence.o]
[compile shu-encseq-gc.o]
[compile shu-genomediff.o]
[compile shu_unitfile.o]
[compile spaced-seeds.o]
[compile specialrank.o]
[compile spmsuftab.o]
[compile squarededist.o]
[compile substriter.o]
[compile tagerator.o]
[compile test-mappedstr.o]
[compile test-maxpairs.o]
[compile test-mergeesa.o]
[compile test-mtrieins.o]
[compile test-pairwise.o]
[compile turnwheels.o]
[compile twobits2kmers.o]
[compile tyr-map.o]
[compile tyr-mersplit.o]
[compile tyr-mkindex.o]
[compile tyr-occratio.o]
[compile tyr-search.o]
[compile xdrop.o]
[compile ags.o]
[compile ags_build.o]
[compile align_dna.o]
[compile align_protein.o]
[compile backtrace_path.o]
[compile bssm_helper.o]
[compile bssm_param.o]
[compile bssm_param_rmsd.o]
[compile bssm_seq_processor.o]
[compile bssm_train_stream.o]
[compile bssm_train_visitor.o]
[compile call_info.o]
[compile chain_collection.o]
[compile chaining.o]
[compile compute_scores.o]
[compile desc_cache.o]
[compile dp_options_core.o]
[compile dp_options_est.o]
[compile dp_options_postpro.o]
[compile dp_param.o]
[compile dp_scores_protein.o]
[compile editoperation.o]
[compile gff3_pgl_visitor.o]
[compile gff3_sa_visitor.o]
[compile gt_gth.o]
[compile gt_gthbssmbuild.o]
[compile gt_gthbssmfileinfo.o]
[compile gt_gthbssmprint.o]
[compile gt_gthbssmrmsd.o]
[compile gt_gthbssmtrain.o]
[compile gt_gthconsensus.o]
[compile gt_gthfilestat.o]
[compile gt_gthmkbssmfiles.o]
[compile gt_gthsplit.o]
[compile gthalignment.o]
[compile gthchain.o]
[compile gthcluster.o]
[compile gthcutoffsminimal.o]
[compile gthcutoffsrelaxed.o]
[compile gthcutoffsstrict.o]
[compile gthmatch.o]
[compile gthorf.o]
[compile gthoutput.o]
[compile gthsadistri.o]
[compile gthsortags.o]
[compile gthsplicesitescr.o]
[compile gthtrans.o]
[compile gthtravalign.o]
[compile gthverbosefunc.o]
[compile gthverbosefuncvm.o]
[compile gthxml.o]
[compile indent.o]
[compile input.o]
[compile intermediate.o]
[compile md5_cache.o]
[compile parse_options.o]
[compile path_matrix.o]
[compile path_walker.o]
[compile pgl.o]
[compile pgl_collection.o]
[compile pgl_visitor.o]
[compile proc_sa_collection.o]
[compile region_factory.o]
[compile run_header.o]
[compile sa.o]
[compile sa_cmp.o]
[compile sa_collection.o]
[compile sa_filter.o]
[compile sa_visitor.o]
[compile seq_con.o]
[compile similarity_filter.o]
[compile splice_site_model.o]
[compile spliced_seq.o]
[compile stat.o]
[compile time.o]
[compile txt_pgl_visitor.o]
[compile txt_sa_visitor.o]
[compile xml_final_sa_visitor.o]
[compile xml_inter_sa_visitor.o]
[compile xml_pgl_visitor.o]
[compile gt_ltrclustering.o]
[compile gt_ltrdigest.o]
[compile gt_ltrharvest.o]
[compile ltr_classify_stream.o]
[compile ltr_cluster_prepare_seq_visitor.o]
[compile ltr_cluster_stream.o]
[compile ltr_four_char_motif.o]
[compile ltr_input_check_visitor.o]
[compile ltr_orf_annotator_stream.o]
[compile ltr_refseq_match_stream.o]
[compile ltrdigest_file_out_stream.o]
[compile ltrdigest_pbs_visitor.o]
[compile ltrdigest_pdom_visitor.o]
[compile ltrdigest_ppt_visitor.o]
[compile ltrdigest_strand_assign_visitor.o]
[compile ltrharvest_fasta_out_stream.o]
[compile ltrharvest_fasta_out_visitor.o]
[compile ltrharvest_stream.o]
[compile ltrharvest_tabout_stream.o]
[compile ltrharvest_tabout_visitor.o]
[compile pdom_model_set.o]
[compile metagenomethreader.o]
[compile mg_codon.o]
[compile mg_combinedscore.o]
[compile mg_compute_gene_prediction.o]
[compile mg_computepath.o]
[compile mg_outputwriter.o]
[compile mg_reverse.o]
[compile mg_xmlparser.o]
[compile block.o]
[compile canvas.o]
[compile canvas_cairo.o]
[compile canvas_cairo_context.o]
[compile canvas_cairo_file.o]
[compile color.o]
[compile coords.o]
[compile custom_track.o]
[compile custom_track_example.o]
[compile custom_track_gc_content.o]
[compile custom_track_script_wrapper.o]
[compile diagram.o]
[compile drawing_range.o]
[compile element.o]
[compile graphics.o]
[compile graphics_cairo.o]
[compile gt_sketch.o]
[compile gt_sketch_page.o]
[compile image_info.o]
[compile layout.o]
[compile line.o]
[compile line_breaker.o]
[compile line_breaker_bases.o]
[compile line_breaker_captions.o]
[compile luastyle.o]
[compile rec_map.o]
[compile style.o]
[compile text_width_calculator.o]
[compile text_width_calculator_cairo.o]
[compile track.o]
[link libgenometools.a]
ar: creating lib/libgenometools.a
[gathering public API symbols to obj/public_symbols.lst]
[link libgenometools.so]
[compile gt.o]
[compile gtr.o]
[compile gtt.o]
[compile interactive.o]
[compile gt_bed_to_gff3.o]
[compile gt_cds.o]
[compile gt_chain2dim.o]
[compile gt_chseqids.o]
[compile gt_clean.o]
[compile gt_compreads.o]
[compile gt_compreads_compress.o]
[compile gt_compreads_decompress.o]
[compile gt_compreads_refcompress.o]
[compile gt_compreads_refdecompress.o]
[compile gt_compressedbits.o]
[compile gt_condenseq.o]
[compile gt_condenseq_blast.o]
[compile gt_condenseq_compress.o]
[compile gt_condenseq_extract.o]
[compile gt_condenseq_hmmsearch.o]
[compile gt_condenseq_info.o]
[compile gt_condenseq_search.o]
[compile gt_congruence.o]
[compile gt_consensus_sa.o]
[compile gt_convertseq.o]
[compile gt_csa.o]
[compile gt_dev.o]
[compile gt_dot.o]
[compile gt_dupfeat.o]
[compile gt_encseq.o]
[compile gt_encseq2spm.o]
[compile gt_encseq_bench.o]
[compile gt_encseq_bitextract.o]
[compile gt_encseq_check.o]
[compile gt_encseq_decode.o]
[compile gt_encseq_encode.o]
[compile gt_encseq_info.o]
[compile gt_encseq_md5.o]
[compile gt_encseq_sample.o]
[compile gt_eval.o]
[compile gt_extractfeat.o]
[compile gt_extractseq.o]
[compile gt_extracttarget.o]
[compile gt_fastq_sample.o]
[compile gt_featureindex.o]
[compile gt_fingerprint.o]
[compile gt_gdiffcalc.o]
[compile gt_genomediff.o]
[compile gt_gff3.o]
[compile gt_gff3_to_gtf.o]
[compile gt_gff3validator.o]
[compile gt_gtf_to_gff3.o]
[compile gt_guessprot.o]
[compile gt_hop.o]
[compile gt_id_to_md5.o]
[compile gt_idxlocali.o]
[compile gt_inlineseq_add.o]
[compile gt_inlineseq_split.o]
[compile gt_interfeat.o]
[compile gt_kmer_database.o]
[compile gt_linspace_align.o]
[compile gt_loccheck.o]
[compile gt_magicmatch.o]
[compile gt_matchtool.o]
[compile gt_matstat.o]
[compile gt_md5_to_id.o]
[compile gt_merge.o]
[compile gt_mergeesa.o]
[compile gt_mergefeat.o]
[compile gt_mgth.o]
[compile gt_mkfeatureindex.o]
[compile gt_mkfmindex.o]
[compile gt_mmapandread.o]
[compile gt_orffinder.o]
[compile gt_packedindex.o]
[compile gt_packedindex_chk_integrity.o]
[compile gt_packedindex_chk_search.o]
[compile gt_packedindex_mkctxmap.o]
[compile gt_packedindex_trsuftab.o]
[compile gt_paircmp.o]
[compile gt_parsexrf.o]
[compile gt_patternmatch.o]
[compile gt_prebwt.o]
[compile gt_readjoiner.o]
[compile gt_readjoiner_asqg.o]
[compile gt_readjoiner_assembly.o]
[compile gt_readjoiner_cgraph.o]
[compile gt_readjoiner_cnttest.o]
[compile gt_readjoiner_correct.o]
[compile gt_readjoiner_graph.o]
[compile gt_readjoiner_overlap.o]
[compile gt_readjoiner_prefilter.o]
[compile gt_readjoiner_spmtest.o]
[compile gt_readreads.o]
[compile gt_regioncov.o]
[compile gt_repfind.o]
[compile gt_sain.o]
[compile gt_sam_interface.o]
[compile gt_script_filter.o]
[compile gt_seed_extend.o]
[compile gt_select.o]
[compile gt_seq.o]
[compile gt_seqcorrect.o]
[compile gt_seqfilter.o]
[compile gt_seqids.o]
[compile gt_seqlensort.o]
[compile gt_seqmutate.o]
[compile gt_seqorder.o]
[compile gt_seqstat.o]
[compile gt_seqtransform.o]
[compile gt_seqtranslate.o]
[compile gt_sequniq.o]
[compile gt_sfxmap.o]
[compile gt_show_seedext.o]
[compile gt_shredder.o]
[compile gt_shulen.o]
[compile gt_simreads.o]
[compile gt_skproto.o]
[compile gt_snpper.o]
[compile gt_sortbench.o]
[compile gt_speck.o]
[compile gt_splicesiteinfo.o]
[compile gt_splitfasta.o]
[compile gt_stat.o]
[compile gt_suffixerator.o]
[compile gt_tagerator.o]
[compile gt_tallymer.o]
[compile gt_template.o]
[compile gt_tir.o]
[compile gt_trieins.o]
[compile gt_uniq.o]
[compile gt_wtree.o]
[compile gt_wtree_bench.o]
[link gt]
[compile custom_stream.o]
[link custom_stream]
[compile gff3sort.o]
[link gff3sort]
[compile gff3validator.o]
[link gff3validator]
[compile noop.o]
[link noop]
[compile sketch_constructed.o]
[link sketch_constructed]
[compile sketch_parsed_with_ctrack.o]
[link sketch_parsed_with_ctrack]
[compile sketch_parsed_with_ordering.o]
[link sketch_parsed_with_ordering]
[compile sketch_parsed.o]
[link sketch_parsed]
bin/gt gtscripts/gtdoc.lua -html /<<BUILDDIR>>/genometools-1.5.9+ds \
        > www/genometools.org/htdocs/libgenometools.html
bin/gt gtscripts/gtdoc.lua -lua -html /<<BUILDDIR>>/genometools-1.5.9+ds \
        > www/genometools.org/htdocs/docs.html
bin/examples/sketch_parsed gtdata/sketch/default.style \
          www/genometools.org/htdocs/images/parsed.png \
          testdata/eden.gff3
bin/examples/sketch_parsed \
  www/genometools.org/htdocs/annotationsketch/callbacks.style \
  www/genometools.org/htdocs/images/callbacks.png \
          www/genometools.org/htdocs/annotationsketch/callback_examples_with_score.gff3
bin/examples/sketch_constructed gtdata/sketch/default.style \
  www/genometools.org/htdocs/images/constructed.png
mogrify -format jpg +set date:create +set date:modify \
  -define png:exclude-chunk=time \
  www/genometools.org/htdocs/images/*.png && \
  rm -rf www/genometools.org/htdocs/images/*.png
sed -nf scripts/incl.sed \
  www/genometools.org/htdocs/examples_tmpl.html | \
          sed 'N;N;s/\n//' > /tmp/tmp.sed.$$ && \
sed -f /tmp/tmp.sed.$$ \
  www/genometools.org/htdocs/examples_tmpl.html > \
  www/genometools.org/htdocs/examples.html; rm -f /tmp/tmp.sed.$$
bin/gt gtscripts/gtdoc.lua -tex /<<BUILDDIR>>/genometools-1.5.9+ds \
> doc/manuals/api_reference.tex
bin/gt gtscripts/gtdoc.lua -lua -tex /<<BUILDDIR>>/genometools-1.5.9+ds \
> doc/manuals/gtscript_reference.tex
make -C /<<BUILDDIR>>/genometools-1.5.9+ds/doc/devguide
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/devguide'
while (pdflatex --shell-escape devguide ; \
grep -q "Rerun to get cross" devguide.log ) do true ; \
done
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[30]
kpathsea: Running mktextfm cmttb10
mkdir: cannot create directory '././sbuild-nonexistent': Permission denied
mktextfm: /tmp/texfonts/tfm/public/cm/cmttb10.tfm already exists.


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[31] [32] [33] [34] [35] [36] [37]
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[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 array \OT1/ptm/m/n/10.
95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 size \OT
1/ptm/m/n/10.95 must be smaller or equal than
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. \OT1/cmtt/m/n/10.95 GtArrayOutStream \OT1/ptm/m/n/10.95 tak
es an ar-ray of \OT1/cmtt/m/n/10.95 GtGenomeNodes
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[]\OT1/ptm/m/n/10.95 Enables sup-port for loss-less re-pro-duc-tion of the orig
-i-nal se-quence, re-gard-less

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\OT1/ptm/m/n/10.95 of al-pha-bet trans-for-ma-tions that may ap-ply. En-coded s
e-quences cre-ated with-

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\OT1/ptm/m/n/10.95 out this sup-port will not be able to be loaded via a \OT1/c
mtt/m/n/10.95 GtEncseqLoader \OT1/ptm/m/n/10.95 with
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[]\OT1/ptm/m/n/10.95 Reinitializes the given \OT1/cmtt/m/n/10.95 esr \OT1/ptm/m
/n/10.95 with the val-ues as de-scribed in
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\OT1/ptm/m/n/10.95 with the \OT1/cmtt/m/n/10.95 Parent \OT1/ptm/m/n/10.95 and \
OT1/cmtt/m/n/10.95 ID \OT1/ptm/m/n/10.95 at-tributes) are re-al-ized in the C A
PI with the \OT1/cmtt/m/n/10.95 gt[]feature[]node[]add[]child()
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[]\OT1/ptm/m/n/10.95 Delivers the key (in \OT1/cmtt/m/n/10.95 attr[]name\OT1/pt
m/m/n/10.95 )and value (in \OT1/cmtt/m/n/10.95 attr[]value\OT1/ptm/m/n/10.95 ) 
of an at-

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\OT1/ptm/m/n/10.95 tribute. The \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pa-
ram-e-ter car-ries over ar-bi-trary user data from the

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\OT1/cmtt/m/n/10.95 fi\OT1/ptm/m/n/10.95 . Note: The \OT1/cmtt/m/n/10.95 GtFeat
ureStream \OT1/ptm/m/n/10.95 class is now dep-re-cated. Please use the
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[]\OT1/ptm/m/n/10.95 Compare \OT1/cmtt/m/n/10.95 genome[]node[]a \OT1/ptm/m/n/1
0.95 with \OT1/cmtt/m/n/10.95 genome[]node[]b \OT1/ptm/m/n/10.95 and re-turn th
e re-sult (sim-i-lar to
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[]\OT1/ptm/m/n/10.95 Iterate over \OT1/cmtt/m/n/10.95 hashmap \OT1/ptm/m/n/10.9
5 in ei-ther al-pha-bet-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/pt
m/m/n/10.95 was spec-i-

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\OT1/ptm/m/n/10.95 fied as \OT1/cmtt/m/n/10.95 GT[]HASH[]STRING\OT1/ptm/m/n/10.
95 ) or nu-mer-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/ptm/m/n/10.
95 was spec-i-fied as
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtInterFeatureStream \OT1/ptm/m/n/10.
95 in-serts new fea-ture nodes
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\OT1/ptm/m/n/10.95 (trans-fers own-er-ship to \OT1/cmtt/m/n/10.95 genome[]node\
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\OT1/ptm/m/n/10.95 is ex-hausted (0 is re-turned) or an er-ror oc-curs (-1 is r
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\OT1/ptm/m/n/10.95 set). All re-trieved \OT1/cmtt/m/n/10.95 GtGenomeNode\OT1/pt
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\OT1/cmtt/m/n/10.95 gt[]genome[]node[]delete()\OT1/ptm/m/n/10.95 . This method 
is ba-si-cally a con-ve-nience method
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95 w
ith the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/cmtt/
m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and
[129] [130] [131] [132] [133] [134] [135] [136]
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[]\OT1/ptm/m/n/10.95 Return the \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95
 ob-ject if an op-tion named \OT1/cmtt/m/n/10.95 option[]string \OT1/ptm/m/n/10
.95 is present in

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[]\OT1/ptm/m/n/10.95 The \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and \OT
1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-mand li
ne ar-gu-ments
[137] [138] [139] [140] [141] [142] [143] [144]
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\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble reamodes, namely \OT1
/cmtt/m/n/10.95 GT[]READMODE[]FORWARD\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/10.95 G
T[]READMODE[]REVERSE\OT1/ptm/m/n/10.95 ,

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[]\OT1/ptm/m/n/10.95 Returns the \OT1/cmtt/m/n/10.95 GtReadmode \OT1/ptm/m/n/10
.95 for the de-scrip-tion \OT1/cmtt/m/n/10.95 string\OT1/ptm/m/n/10.95 , which 
must be one of
[145] [146]
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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

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\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from
[147] [148]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region
[149] [150] [151] [152]
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[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

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[][][][][] 

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[][][][][][][] 

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[][][][][] 

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[][][][][][][] 
[155]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor
[156] [157]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

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\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

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\OT1/cmtt/m/n/10.95 exon[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/
n/10.95 exon[]number[]distribution\OT1/ptm/m/n/10.95 ,
[158]
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[]\OT1/ptm/m/n/10.95 Set length of \OT1/cmtt/m/n/10.95 str \OT1/ptm/m/n/10.95 t
o \OT1/cmtt/m/n/10.95 length\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 length \OT
1/ptm/m/n/10.95 must be smaller or equal than
[159] [160] [161]
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[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than
[162]
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\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

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[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns
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\OT1/cmtt/m/n/10.95 cairo[]t \OT1/ptm/m/n/10.95 and which should be used later 
via a \OT1/cmtt/m/n/10.95 GtCanvasCairoContext\OT1/ptm/m/n/10.95 , cre-ate a \O
T1/cmtt/m/n/10.95 GtTextWidthCalculatorCairo
[170]
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[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 in the for-mat ""GT[]WD".pointer \OT1/cmtt/m/n/10.95 fp \OT1/pt
m/m/n/10.95 (see

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[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 on \OT1/cmtt/m/n/10.95 fp \OT1/ptm/m/n/10.95 since the last cal
l of

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\OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress() \OT1/ptm/m/n/10.95 or the last 
start of \OT1/cmtt/m/n/10.95 timer\OT1/ptm/m/n/10.95 , along with the cur-rent
[171] [172] [173] [174] [175]
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[]\OT1/ptm/m/n/10.95 Returns a \OT1/cmtt/m/n/10.95 GtStrArray \OT1/ptm/m/n/10.9
5 of trans-la-tion scheme de-scrip-tions, each of the for-mat
[176] [177] [178] [179] [180] [181] [182] [183]
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[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

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[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to
[186]
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[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in $\OML/
ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/it/1
0.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT1/p
tm/m/n/10.95 PATH. 

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[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in the ':
'-separated di-rec-tory list (on Win-

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\OT1/ptm/m/n/10.95 dows ';'-separated) spec-i-fied in en-vi-ron-ment vari-able

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[]\OML/ztmcm/m/it/10.95 ; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/i
t/10.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT
1/cmtt/m/n/10.95 env\OT1/ptm/m/n/10.95 . 

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[]\OT1/ptm/m/n/10.95 Return the (es-ti-mated) to-tal size of all files given in
 \OT1/cmtt/m/n/10.95 filenames\OT1/ptm/m/n/10.95 . Uses

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[]\OT1/ptm/m/n/10.95 Find reg-u-lar ex-e-cutable \OT1/cmtt/m/n/10.95 file \OT1/
ptm/m/n/10.95 in $\OML/ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10
.95 ; \OML/ztmcm/m/it/10.95 set[]todirnameotherwise:Sets[]totheemptystringifreg
ularexecutable[]couldnotbefoundin$\OT1/ptm/m/n/10.95 PATH. 
[187] [188] [189] [190]
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[]\OT1/ptm/m/n/10.95 Prints the log mes-sage ob-tained from for-mat and fol-low
-ing pa-ram-e-ter ac-cord-

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\OT1/ptm/m/n/10.95 ing to if log-ging is en-abled ana-log to\OT1/cmtt/m/n/10.95
 gt[]log[]log()\OT1/ptm/m/n/10.95 . But in con-trast to
[191] [192]
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[]\OT1/ptm/m/n/10.95 This mod-ule im-ple-ments the func-tion\OT1/cmtt/m/n/10.95
 gt[]basename() \OT1/ptm/m/n/10.95 ac-cord-ing to the spec-i-fi-

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\OT1/ptm/m/n/10.95 ca-tions in http://www.unix-systems.org/onlinepubs/7908799/x
sh/basename.html and
[193] [194]
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[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 qsort(3)\OT1/ptm/m/n/10.95 , but 
al-lows an ad-di-tional \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pointer pas
sed to the
[195]
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chapter 1.

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0.95 with \OT1/cmtt/m/n/10.95 genome[]node[]b \OT1/ptm/m/n/10.95 and re-turn th
e re-sult (sim-i-lar to
[98] [99] [100] [101] [102] [103] [104] [105] [106]
Underfull \hbox (badness 2875) in paragraph at lines 7447--7450
[]\OT1/ptm/m/n/10.95 Iterate over \OT1/cmtt/m/n/10.95 hashmap \OT1/ptm/m/n/10.9
5 in ei-ther al-pha-bet-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/pt
m/m/n/10.95 was spec-i-

Underfull \hbox (badness 1762) in paragraph at lines 7447--7450
\OT1/ptm/m/n/10.95 fied as \OT1/cmtt/m/n/10.95 GT[]HASH[]STRING\OT1/ptm/m/n/10.
95 ) or nu-mer-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/ptm/m/n/10.
95 was spec-i-fied as
[107] [108]
Overfull \hbox (1.94502pt too wide) in paragraph at lines 7580--7582
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtInterFeatureStream \OT1/ptm/m/n/10.
95 in-serts new fea-ture nodes
[109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120]
[121] [122] [123] [124]
Underfull \hbox (badness 1655) in paragraph at lines 8934--8940
\OT1/ptm/m/n/10.95 (trans-fers own-er-ship to \OT1/cmtt/m/n/10.95 genome[]node\
OT1/ptm/m/n/10.95 ). If no er-ror oc-curs, 0 is re-turned and

Underfull \hbox (badness 3240) in paragraph at lines 8952--8959
\OT1/ptm/m/n/10.95 is ex-hausted (0 is re-turned) or an er-ror oc-curs (-1 is r
e-turned and \OT1/cmtt/m/n/10.95 err \OT1/ptm/m/n/10.95 is

Underfull \hbox (badness 4266) in paragraph at lines 8952--8959
\OT1/ptm/m/n/10.95 set). All re-trieved \OT1/cmtt/m/n/10.95 GtGenomeNode\OT1/pt
m/m/n/10.95 s are deleted au-to-mat-i-cally with calls to

Underfull \hbox (badness 2828) in paragraph at lines 8952--8959
\OT1/cmtt/m/n/10.95 gt[]genome[]node[]delete()\OT1/ptm/m/n/10.95 . This method 
is ba-si-cally a con-ve-nience method
[125] [126] [127] [128]
Underfull \hbox (badness 2856) in paragraph at lines 9240--9242
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9256--9258
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9273--9276
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9292--9296
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9310--9314
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9328--9330
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9345--9348
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9363--9366
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9382--9386
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9400--9402
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9417--9420
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9435--9438
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9454--9458
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9472--9474
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9488--9490
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9505--9508
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9524--9528
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9605--9609
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9625--9630
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9644--9646
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9659--9661
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 9676--9679
[]\OT1/ptm/m/n/10.95 Return a \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95 w
ith the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/cmtt/
m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9708--9710
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and
[129] [130] [131] [132] [133] [134] [135] [136]
Underfull \hbox (badness 1496) in paragraph at lines 10033--10035
[]\OT1/ptm/m/n/10.95 Return the \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95
 ob-ject if an op-tion named \OT1/cmtt/m/n/10.95 option[]string \OT1/ptm/m/n/10
.95 is present in

Underfull \hbox (badness 5446) in paragraph at lines 10153--10155
[]\OT1/ptm/m/n/10.95 The \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and \OT
1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-mand li
ne ar-gu-ments
[137] [138] [139] [140] [141] [142] [143] [144]
Overfull \hbox (37.97119pt too wide) in paragraph at lines 10686--10688
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble reamodes, namely \OT1
/cmtt/m/n/10.95 GT[]READMODE[]FORWARD\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/10.95 G
T[]READMODE[]REVERSE\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 2626) in paragraph at lines 10713--10716
[]\OT1/ptm/m/n/10.95 Returns the \OT1/cmtt/m/n/10.95 GtReadmode \OT1/ptm/m/n/10
.95 for the de-scrip-tion \OT1/cmtt/m/n/10.95 string\OT1/ptm/m/n/10.95 , which 
must be one of
[145] [146]
Underfull \hbox (badness 2735) in paragraph at lines 10873--10876
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

Underfull \hbox (badness 10000) in paragraph at lines 10889--10895
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

Underfull \hbox (badness 1189) in paragraph at lines 10889--10895
\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from
[147] [148]
Overfull \hbox (1.85855pt too wide) in paragraph at lines 11030--11032
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region
[149] [150] [151] [152]
Overfull \vbox (13.10382pt too high) has occurred while \output is active
[153] [154]
Underfull \hbox (badness 2698) in paragraph at lines 11409--11411
[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

Overfull \hbox (4.98322pt too wide) in paragraph at lines 11418--11419
[][][][][] 

Overfull \hbox (10.6532pt too wide) in paragraph at lines 11419--11420
[][][][][][][] 

Overfull \hbox (27.66315pt too wide) in paragraph at lines 11445--11446
[][][][][] 

Overfull \hbox (33.33313pt too wide) in paragraph at lines 11446--11447
[][][][][][][] 
[155]
Overfull \hbox (58.46886pt too wide) in paragraph at lines 11485--11488
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor
[156] [157]
Overfull \hbox (31.52028pt too wide) in paragraph at lines 11643--11646
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

Underfull \hbox (badness 3668) in paragraph at lines 11665--11673
\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 11665--11673
\OT1/cmtt/m/n/10.95 exon[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/
n/10.95 exon[]number[]distribution\OT1/ptm/m/n/10.95 ,
[158]
Underfull \hbox (badness 5667) in paragraph at lines 11902--11904
[]\OT1/ptm/m/n/10.95 Set length of \OT1/cmtt/m/n/10.95 str \OT1/ptm/m/n/10.95 t
o \OT1/cmtt/m/n/10.95 length\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 length \OT
1/ptm/m/n/10.95 must be smaller or equal than
[159] [160] [161]
Underfull \hbox (badness 2564) in paragraph at lines 12080--12082
[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than
[162]
Overfull \hbox (21.75429pt too wide) in paragraph at lines 12123--12126
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 12149--12151
[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns
[163] [164] [165] [166] [167] [168] [169]
Overfull \hbox (83.5338pt too wide) in paragraph at lines 12771--12777
\OT1/cmtt/m/n/10.95 cairo[]t \OT1/ptm/m/n/10.95 and which should be used later 
via a \OT1/cmtt/m/n/10.95 GtCanvasCairoContext\OT1/ptm/m/n/10.95 , cre-ate a \O
T1/cmtt/m/n/10.95 GtTextWidthCalculatorCairo
[170]
Underfull \hbox (badness 3168) in paragraph at lines 12923--12927
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 in the for-mat ""GT[]WD".pointer \OT1/cmtt/m/n/10.95 fp \OT1/pt
m/m/n/10.95 (see

Underfull \hbox (badness 10000) in paragraph at lines 12971--12975
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 on \OT1/cmtt/m/n/10.95 fp \OT1/ptm/m/n/10.95 since the last cal
l of

Underfull \hbox (badness 1292) in paragraph at lines 12971--12975
\OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress() \OT1/ptm/m/n/10.95 or the last 
start of \OT1/cmtt/m/n/10.95 timer\OT1/ptm/m/n/10.95 , along with the cur-rent
[171] [172] [173] [174] [175]
Underfull \hbox (badness 2035) in paragraph at lines 13319--13323
[]\OT1/ptm/m/n/10.95 Returns a \OT1/cmtt/m/n/10.95 GtStrArray \OT1/ptm/m/n/10.9
5 of trans-la-tion scheme de-scrip-tions, each of the for-mat
[176] [177] [178] [179] [180] [181] [182] [183]
Underfull \hbox (badness 10000) in paragraph at lines 13923--13924


Underfull \hbox (badness 10000) in paragraph at lines 13935--13936

[184] [185]
Underfull \hbox (badness 3364) in paragraph at lines 14150--14155
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

Underfull \hbox (badness 3364) in paragraph at lines 14188--14193
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to
[186]
Overfull \hbox (183.05757pt too wide) in paragraph at lines 14288--14290
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in $\OML/
ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/it/1
0.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT1/p
tm/m/n/10.95 PATH. 

Underfull \hbox (badness 10000) in paragraph at lines 14304--14308
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in the ':
'-separated di-rec-tory list (on Win-

Underfull \hbox (badness 10000) in paragraph at lines 14304--14308
\OT1/ptm/m/n/10.95 dows ';'-separated) spec-i-fied in en-vi-ron-ment vari-able

Overfull \hbox (105.20361pt too wide) in paragraph at lines 14304--14308
[]\OML/ztmcm/m/it/10.95 ; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/i
t/10.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT
1/cmtt/m/n/10.95 env\OT1/ptm/m/n/10.95 . 

Underfull \hbox (badness 5091) in paragraph at lines 14333--14335
[]\OT1/ptm/m/n/10.95 Return the (es-ti-mated) to-tal size of all files given in
 \OT1/cmtt/m/n/10.95 filenames\OT1/ptm/m/n/10.95 . Uses

Overfull \hbox (344.88547pt too wide) in paragraph at lines 14365--14368
[]\OT1/ptm/m/n/10.95 Find reg-u-lar ex-e-cutable \OT1/cmtt/m/n/10.95 file \OT1/
ptm/m/n/10.95 in $\OML/ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10
.95 ; \OML/ztmcm/m/it/10.95 set[]todirnameotherwise:Sets[]totheemptystringifreg
ularexecutable[]couldnotbefoundin$\OT1/ptm/m/n/10.95 PATH. 
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chapter 1.

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9292--9296
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9310--9314
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9328--9330
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9345--9348
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9363--9366
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9382--9386
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9400--9402
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9454--9458
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9524--9528
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 9676--9679
[]\OT1/ptm/m/n/10.95 Return a \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95 w
ith the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/cmtt/
m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 2856) in paragraph at lines 9708--9710
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and
[129] [130] [131] [132] [133] [134] [135] [136]
Underfull \hbox (badness 1496) in paragraph at lines 10033--10035
[]\OT1/ptm/m/n/10.95 Return the \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95
 ob-ject if an op-tion named \OT1/cmtt/m/n/10.95 option[]string \OT1/ptm/m/n/10
.95 is present in

Underfull \hbox (badness 5446) in paragraph at lines 10153--10155
[]\OT1/ptm/m/n/10.95 The \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and \OT
1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-mand li
ne ar-gu-ments
[137] [138] [139] [140] [141] [142] [143] [144]
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\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble reamodes, namely \OT1
/cmtt/m/n/10.95 GT[]READMODE[]FORWARD\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/10.95 G
T[]READMODE[]REVERSE\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 2626) in paragraph at lines 10713--10716
[]\OT1/ptm/m/n/10.95 Returns the \OT1/cmtt/m/n/10.95 GtReadmode \OT1/ptm/m/n/10
.95 for the de-scrip-tion \OT1/cmtt/m/n/10.95 string\OT1/ptm/m/n/10.95 , which 
must be one of
[145] [146]
Underfull \hbox (badness 2735) in paragraph at lines 10873--10876
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

Underfull \hbox (badness 10000) in paragraph at lines 10889--10895
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

Underfull \hbox (badness 1189) in paragraph at lines 10889--10895
\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from
[147] [148]
Overfull \hbox (1.85855pt too wide) in paragraph at lines 11030--11032
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region
[149] [150] [151] [152]
Overfull \vbox (13.10382pt too high) has occurred while \output is active
[153] [154]
Underfull \hbox (badness 2698) in paragraph at lines 11409--11411
[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

Overfull \hbox (4.98322pt too wide) in paragraph at lines 11418--11419
[][][][][] 

Overfull \hbox (10.6532pt too wide) in paragraph at lines 11419--11420
[][][][][][][] 

Overfull \hbox (27.66315pt too wide) in paragraph at lines 11445--11446
[][][][][] 

Overfull \hbox (33.33313pt too wide) in paragraph at lines 11446--11447
[][][][][][][] 
[155]
Overfull \hbox (58.46886pt too wide) in paragraph at lines 11485--11488
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor
[156] [157]
Overfull \hbox (31.52028pt too wide) in paragraph at lines 11643--11646
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

Underfull \hbox (badness 3668) in paragraph at lines 11665--11673
\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 11665--11673
\OT1/cmtt/m/n/10.95 exon[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/
n/10.95 exon[]number[]distribution\OT1/ptm/m/n/10.95 ,
[158]
Underfull \hbox (badness 5667) in paragraph at lines 11902--11904
[]\OT1/ptm/m/n/10.95 Set length of \OT1/cmtt/m/n/10.95 str \OT1/ptm/m/n/10.95 t
o \OT1/cmtt/m/n/10.95 length\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 length \OT
1/ptm/m/n/10.95 must be smaller or equal than
[159] [160] [161]
Underfull \hbox (badness 2564) in paragraph at lines 12080--12082
[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than
[162]
Overfull \hbox (21.75429pt too wide) in paragraph at lines 12123--12126
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 12149--12151
[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns
[163] [164] [165] [166] [167] [168] [169]
Overfull \hbox (83.5338pt too wide) in paragraph at lines 12771--12777
\OT1/cmtt/m/n/10.95 cairo[]t \OT1/ptm/m/n/10.95 and which should be used later 
via a \OT1/cmtt/m/n/10.95 GtCanvasCairoContext\OT1/ptm/m/n/10.95 , cre-ate a \O
T1/cmtt/m/n/10.95 GtTextWidthCalculatorCairo
[170]
Underfull \hbox (badness 3168) in paragraph at lines 12923--12927
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 in the for-mat ""GT[]WD".pointer \OT1/cmtt/m/n/10.95 fp \OT1/pt
m/m/n/10.95 (see

Underfull \hbox (badness 10000) in paragraph at lines 12971--12975
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 on \OT1/cmtt/m/n/10.95 fp \OT1/ptm/m/n/10.95 since the last cal
l of

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\OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress() \OT1/ptm/m/n/10.95 or the last 
start of \OT1/cmtt/m/n/10.95 timer\OT1/ptm/m/n/10.95 , along with the cur-rent
[171] [172] [173] [174] [175]
Underfull \hbox (badness 2035) in paragraph at lines 13319--13323
[]\OT1/ptm/m/n/10.95 Returns a \OT1/cmtt/m/n/10.95 GtStrArray \OT1/ptm/m/n/10.9
5 of trans-la-tion scheme de-scrip-tions, each of the for-mat
[176] [177] [178] [179] [180] [181] [182] [183]
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Underfull \hbox (badness 10000) in paragraph at lines 13935--13936

[184] [185]
Underfull \hbox (badness 3364) in paragraph at lines 14150--14155
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

Underfull \hbox (badness 3364) in paragraph at lines 14188--14193
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to
[186]
Overfull \hbox (183.05757pt too wide) in paragraph at lines 14288--14290
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in $\OML/
ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/it/1
0.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT1/p
tm/m/n/10.95 PATH. 

Underfull \hbox (badness 10000) in paragraph at lines 14304--14308
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in the ':
'-separated di-rec-tory list (on Win-

Underfull \hbox (badness 10000) in paragraph at lines 14304--14308
\OT1/ptm/m/n/10.95 dows ';'-separated) spec-i-fied in en-vi-ron-ment vari-able

Overfull \hbox (105.20361pt too wide) in paragraph at lines 14304--14308
[]\OML/ztmcm/m/it/10.95 ; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/i
t/10.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT
1/cmtt/m/n/10.95 env\OT1/ptm/m/n/10.95 . 

Underfull \hbox (badness 5091) in paragraph at lines 14333--14335
[]\OT1/ptm/m/n/10.95 Return the (es-ti-mated) to-tal size of all files given in
 \OT1/cmtt/m/n/10.95 filenames\OT1/ptm/m/n/10.95 . Uses

Overfull \hbox (344.88547pt too wide) in paragraph at lines 14365--14368
[]\OT1/ptm/m/n/10.95 Find reg-u-lar ex-e-cutable \OT1/cmtt/m/n/10.95 file \OT1/
ptm/m/n/10.95 in $\OML/ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10
.95 ; \OML/ztmcm/m/it/10.95 set[]todirnameotherwise:Sets[]totheemptystringifreg
ularexecutable[]couldnotbefoundin$\OT1/ptm/m/n/10.95 PATH. 
[187] [188] [189] [190]
Underfull \hbox (badness 2065) in paragraph at lines 14567--14571
[]\OT1/ptm/m/n/10.95 Prints the log mes-sage ob-tained from for-mat and fol-low
-ing pa-ram-e-ter ac-cord-

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\OT1/ptm/m/n/10.95 ing to if log-ging is en-abled ana-log to\OT1/cmtt/m/n/10.95
 gt[]log[]log()\OT1/ptm/m/n/10.95 . But in con-trast to
[191] [192]
Underfull \hbox (badness 2762) in paragraph at lines 14750--14760
[]\OT1/ptm/m/n/10.95 This mod-ule im-ple-ments the func-tion\OT1/cmtt/m/n/10.95
 gt[]basename() \OT1/ptm/m/n/10.95 ac-cord-ing to the spec-i-fi-

Underfull \hbox (badness 2951) in paragraph at lines 14750--14760
\OT1/ptm/m/n/10.95 ca-tions in http://www.unix-systems.org/onlinepubs/7908799/x
sh/basename.html and
[193] [194]
Underfull \hbox (badness 10000) in paragraph at lines 14888--14890
[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 qsort(3)\OT1/ptm/m/n/10.95 , but 
al-lows an ad-di-tional \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pointer pas
sed to the
[195]
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[196] [197] [198] [199] [200]) [201] (./annotationsketch.aux)

LaTeX Font Warning: Some font shapes were not available, defaults substituted.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/p
ublic/cm/cmttb10.540pk> </tmp/texfonts/pk/ljfour/public/cm/cmttb10.864pk> </tmp
/texfonts/pk/ljfour/public/cm/cmttb10.480pk>{/usr/share/texlive/texmf-dist/font
s/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm
/cmssbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cms
y10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt8.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/
texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1
/urw/times/utmri8a.pfb>
Output written on annotationsketch.pdf (201 pages, 1327699 bytes).
Transcript written on annotationsketch.log.
mv annotationsketch.aux annotationsketch-pdf.aux
test -e annotationsketch.bbl && mv annotationsketch.bbl annotationsketch-pdf.bbl
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test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
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make[3]: [readjoiner-pdf.aux] Error 1 (ignored)
pdflatex readjoiner.tex && rm readjoiner.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./readjoiner.tex
LaTeX2e <2016/03/31> patch level 1
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
No file readjoiner.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
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LaTeX Warning: Citation `MYE:2005' on page 1 undefined on input line 56.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 59.


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[] 

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[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
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[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2]

LaTeX Warning: Citation `MYE:2005' on page 3 undefined on input line 210.

[3]

LaTeX Warning: Citation `MYE:2005' on page 4 undefined on input line 260.

[4]

LaTeX Warning: Citation `Edena' on page 5 undefined on input line 327.

[5] [6] [7] (./readjoiner.aux)

LaTeX Warning: There were undefined references.


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

 )
(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/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 109479 bytes).
Transcript written on readjoiner.log.
mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
bibtex readjoiner
This is BibTeX, Version 0.99d (TeX Live 2016/Debian)
The top-level auxiliary file: readjoiner.aux
I found no \bibdata command---while reading file readjoiner.aux
I found no \bibstyle command---while reading file readjoiner.aux
(There were 2 error messages)
Makefile:32: recipe for target 'readjoiner-pdf.bbl' failed
make[3]: [readjoiner-pdf.bbl] Error 2 (ignored)
test -e readjoiner-pdf.bbl || touch readjoiner-pdf.bbl
diff readjoiner-pdf.bbl readjoiner.bbl || mv readjoiner.bbl readjoiner-pdf.bbl && rm -f readjoiner.bbl
mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
test -e readjoiner-pdf.bbl && mv readjoiner-pdf.bbl readjoiner.bbl
pdflatex readjoiner.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./readjoiner.tex
LaTeX2e <2016/03/31> patch level 1
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./readjoiner.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (6.12744pt too wide) in paragraph at lines 64--74
[] 

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[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
Underfull \hbox (badness 4132) in paragraph at lines 184--187
[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2] [3] [4] [5] [6] [7] (./readjoiner.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/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 108814 bytes).
Transcript written on readjoiner.log.
pdflatex readjoiner.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./readjoiner.tex
LaTeX2e <2016/03/31> patch level 1
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/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/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./readjoiner.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (6.12744pt too wide) in paragraph at lines 64--74
[] 

Overfull \hbox (19.25665pt too wide) in paragraph at lines 79--82
[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
Underfull \hbox (badness 4132) in paragraph at lines 184--187
[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2] [3] [4] [5] [6] [7] (./readjoiner.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/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 108814 bytes).
Transcript written on readjoiner.log.
mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner.bbl && mv readjoiner.bbl readjoiner-pdf.bbl
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
Makefile:39: recipe for target 'hop-pdf.aux' failed
make[3]: [hop-pdf.aux] Error 1 (ignored)
pdflatex hop.tex && rm hop.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./hop.tex
LaTeX2e <2016/03/31> patch level 1
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/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/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
No file hop.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `HOP' on page 1 undefined on input line 41.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 70.

[1]
Overfull \hbox (37.48308pt too wide) in paragraph at lines 131--139
[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

Overfull \hbox (32.30313pt too wide) in paragraph at lines 145--145
[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (14.55139pt too wide) in paragraph at lines 207--212
\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
[3] [4] (./hop.aux)

LaTeX Warning: There were undefined references.


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

 )
(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/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on hop.pdf (5 pages, 74416 bytes).
Transcript written on hop.log.
mv hop.aux hop-pdf.aux
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
bibtex hop
This is BibTeX, Version 0.99d (TeX Live 2016/Debian)
The top-level auxiliary file: hop.aux
I found no \bibdata command---while reading file hop.aux
I found no \bibstyle command---while reading file hop.aux
(There were 2 error messages)
Makefile:32: recipe for target 'hop-pdf.bbl' failed
make[3]: [hop-pdf.bbl] Error 2 (ignored)
test -e hop-pdf.bbl || touch hop-pdf.bbl
diff hop-pdf.bbl hop.bbl || mv hop.bbl hop-pdf.bbl && rm -f hop.bbl
mv hop.aux hop-pdf.aux
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
test -e hop-pdf.bbl && mv hop-pdf.bbl hop.bbl
pdflatex hop.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./hop.tex
LaTeX2e <2016/03/31> patch level 1
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/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/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./hop.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [1]
Overfull \hbox (37.48308pt too wide) in paragraph at lines 131--139
[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

Overfull \hbox (32.30313pt too wide) in paragraph at lines 145--145
[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (14.55139pt too wide) in paragraph at lines 207--212
\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
[3] [4] (./hop.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/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on hop.pdf (5 pages, 73817 bytes).
Transcript written on hop.log.
pdflatex hop.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./hop.tex
LaTeX2e <2016/03/31> patch level 1
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/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/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
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(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./hop.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [1]
Overfull \hbox (37.48308pt too wide) in paragraph at lines 131--139
[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

Overfull \hbox (32.30313pt too wide) in paragraph at lines 145--145
[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
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\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
[3] [4] (./hop.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/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
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Transcript written on hop.log.
mv hop.aux hop-pdf.aux
test -e hop.bbl && mv hop.bbl hop-pdf.bbl
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
Makefile:39: recipe for target 'ltrharvest-pdf.aux' failed
make[3]: [ltrharvest-pdf.aux] Error 1 (ignored)
pdflatex ltrharvest.tex && rm ltrharvest.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrharvest.tex
LaTeX2e <2016/03/31> patch level 1
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
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LaTeX Warning: Citation `LTRharvesturl' on page 1 undefined on input line 50.


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[1] [2]

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[3] [4] [5]

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[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
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[8]
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[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) TSD l(TSD) m(l
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tr 100 -maxlenltr 1000 
[9]

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[10]
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[]\OT1/ptm/m/sc/12 GFF3\OT1/ptm/m/n/12 , tab de-lim-ited file for-mat for genom
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[11] [12] (./ltrharvest.aux)

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 )
(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/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/t
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b></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrharvest.pdf (13 pages, 160859 bytes).
Transcript written on ltrharvest.log.
mv ltrharvest.aux ltrharvest-pdf.aux
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
bibtex ltrharvest
This is BibTeX, Version 0.99d (TeX Live 2016/Debian)
The top-level auxiliary file: ltrharvest.aux
I found no \bibdata command---while reading file ltrharvest.aux
I found no \bibstyle command---while reading file ltrharvest.aux
(There were 2 error messages)
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test -e ltrharvest-pdf.bbl || touch ltrharvest-pdf.bbl
diff ltrharvest-pdf.bbl ltrharvest.bbl || mv ltrharvest.bbl ltrharvest-pdf.bbl && rm -f ltrharvest.bbl
mv ltrharvest.aux ltrharvest-pdf.aux
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
test -e ltrharvest-pdf.bbl && mv ltrharvest-pdf.bbl ltrharvest.bbl
pdflatex ltrharvest.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrharvest.tex
LaTeX2e <2016/03/31> patch level 1
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
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*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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[8]
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[9] [10]
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[]\OT1/ptm/m/sc/12 GFF3\OT1/ptm/m/n/12 , tab de-lim-ited file for-mat for genom
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[11] [12] (./ltrharvest.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
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/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/te
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b></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrharvest.pdf (13 pages, 160033 bytes).
Transcript written on ltrharvest.log.
pdflatex ltrharvest.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrharvest.tex
LaTeX2e <2016/03/31> patch level 1
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
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(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
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(./ltrharvest.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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nts/map/pdftex/updmap/pdftex.map}]
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[8]
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[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) TSD l(TSD) m(l
LTR) s(rLTR) e(rLTR) l(rLTR) TSD l(TSD) m(rLTR) sim(LTRs) seq-nr[] 

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tr 100 -maxlenltr 1000 
[9] [10]
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[]\OT1/ptm/m/sc/12 GFF3\OT1/ptm/m/n/12 , tab de-lim-ited file for-mat for genom
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(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
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cm/cmmi6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
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/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/te
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Transcript written on ltrharvest.log.
mv ltrharvest.aux ltrharvest-pdf.aux
test -e ltrharvest.bbl && mv ltrharvest.bbl ltrharvest-pdf.bbl
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
Makefile:39: recipe for target 'ltrdigest-pdf.aux' failed
make[3]: [ltrdigest-pdf.aux] Error 1 (ignored)
pdflatex ltrdigest.tex && rm ltrdigest.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
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entering extended mode
(./ltrdigest.tex
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Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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[]].
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
/ptm/m/n/12 type) and the pre-dicted LTRs (\OT1/pcr/m/n/12 long[]terminal[]repe
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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
 genome.fas 

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[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
 \OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

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\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
[9] [10] (./ltrdigest.aux)

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Transcript written on ltrdigest.log.
mv ltrdigest.aux ltrdigest-pdf.aux
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
bibtex ltrdigest
This is BibTeX, Version 0.99d (TeX Live 2016/Debian)
The top-level auxiliary file: ltrdigest.aux
The style file: unsrt.bst
I found no \bibdata command---while reading file ltrdigest.aux
Warning--I didn't find a database entry for "EKW07"
Warning--I didn't find a database entry for "gff3"
Warning--I didn't find a database entry for "genometools"
Warning--I didn't find a database entry for "hmmer"
Warning--I didn't find a database entry for "pfam"
(There was 1 error message)
Makefile:32: recipe for target 'ltrdigest-pdf.bbl' failed
make[3]: [ltrdigest-pdf.bbl] Error 2 (ignored)
test -e ltrdigest-pdf.bbl || touch ltrdigest-pdf.bbl
diff ltrdigest-pdf.bbl ltrdigest.bbl || mv ltrdigest.bbl ltrdigest-pdf.bbl && rm -f ltrdigest.bbl
0a1,3
> \begin{thebibliography}{}
> 
> \end{thebibliography}
mv ltrdigest.aux ltrdigest-pdf.aux
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
test -e ltrdigest-pdf.bbl && mv ltrdigest-pdf.bbl ltrdigest.bbl
pdflatex ltrdigest.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
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entering extended mode
(./ltrdigest.tex
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\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
-di-dates, like those re-ported by\OT1/ptm/m/it/12 LTRharvest \OT1/ptm/m/n/12 [
[]].
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
/ptm/m/n/12 type) and the pre-dicted LTRs (\OT1/pcr/m/n/12 long[]terminal[]repe
at

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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
 genome.fas 

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[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
 \OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

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\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
[9] [10] (./ltrdigest.aux) )
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Output written on ltrdigest.pdf (11 pages, 185006 bytes).
Transcript written on ltrdigest.log.
pdflatex ltrdigest.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
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entering extended mode
(./ltrdigest.tex
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Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
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[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
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\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
-di-dates, like those re-ported by\OT1/ptm/m/it/12 LTRharvest \OT1/ptm/m/n/12 [
[]].
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
/ptm/m/n/12 type) and the pre-dicted LTRs (\OT1/pcr/m/n/12 long[]terminal[]repe
at

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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
 genome.fas 

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[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
 \OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

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\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
[9] [10] (./ltrdigest.aux) )
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Output written on ltrdigest.pdf (11 pages, 185006 bytes).
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mv ltrdigest.aux ltrdigest-pdf.aux
test -e ltrdigest.bbl && mv ltrdigest.bbl ltrdigest-pdf.bbl
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
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mv uniquesub.aux uniquesub-pdf.aux
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bibtex uniquesub
This is BibTeX, Version 0.99d (TeX Live 2016/Debian)
The top-level auxiliary file: uniquesub.aux
I found no \bibdata command---while reading file uniquesub.aux
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pdflatex uniquesub.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
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\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
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[1]

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d BLAST-hit file, \OT1/pcr/m/n/10.95 Metagenome-Filename \OT1/ptm/m/n/12 the FA
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Transcript written on packedindex.log.
mv packedindex.aux packedindex-pdf.aux
test -e packedindex-pdf.aux && mv packedindex-pdf.aux packedindex.aux
bibtex packedindex
This is BibTeX, Version 0.99d (TeX Live 2016/Debian)
The top-level auxiliary file: packedindex.aux
The style file: unsrt.bst
Database file #1: gtmanuals.bib
test -e packedindex-pdf.bbl || touch packedindex-pdf.bbl
diff packedindex-pdf.bbl packedindex.bbl || mv packedindex.bbl packedindex-pdf.bbl && rm -f packedindex.bbl
0a1,21
> \begin{thebibliography}{1}
> 
> \bibitem{oai:CiteSeerPSU:481302}
> Paolo Ferragina and Giovanni Manzini.
> \newblock Opportunistic data structures with applications, September~03 2000.
> 
> \bibitem{journals/talg/FerraginaMMN07}
> Paolo Ferragina, Giovanni Manzini, Veli M{\"a}kinen, and Gonzalo Navarro.
> \newblock Compressed representations of sequences and full-text indexes.
> \newblock {\em ACM Transactions on Algorithms}, 3(2), 2007.
> 
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
> 
> \bibitem{gttestdata}
> \textsc{GenomeTools} test data set.
> \newblock \url{git://genometools.org/gttestdata.git}.
> 
> \end{thebibliography}
mv packedindex.aux packedindex-pdf.aux
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This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
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\OT1/ptm/m/n/12 The \OT1/pcr/b/n/12 mkctxmap \OT1/ptm/m/n/12 sub-tool fa-cil-i-
tates late build-ing of a re-verse lookup ta-ble, it can use the \OT1/pcr/m/sl/
12 prefix.suf
[3] [4]

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[]\OT1/ptm/m/n/12 First com-pute the \OT1/ptm/m/it/12 packedin-dex \OT1/ptm/m/n
/12 in-dex file (this as-sumes \OT1/pcr/m/sl/12 chr01.19960731.fsa.gz \OT1/ptm/
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\OT1/ptm/m/n/12 The \OT1/pcr/b/n/12 mkctxmap \OT1/ptm/m/n/12 sub-tool fa-cil-i-
tates late build-ing of a re-verse lookup ta-ble, it can use the \OT1/pcr/m/sl/
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/12 in-dex file (this as-sumes \OT1/pcr/m/sl/12 chr01.19960731.fsa.gz \OT1/ptm/
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r, C., Stoye, J., Giegerich,

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This is BibTeX, Version 0.99d (TeX Live 2016/Debian)
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[]\OT1/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
r, C., Stoye, J., Giegerich,
[4] (./repfind.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/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
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m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy8.pfb></
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Output written on repfind.pdf (4 pages, 103366 bytes).
Transcript written on repfind.log.
mv repfind.aux repfind-pdf.aux
test -e repfind.bbl && mv repfind.bbl repfind-pdf.bbl
head -n 6999 ../../testdata/at1MB > read1.fna
echo ">" > read2.fna
tail -n 6945 ../../testdata/at1MB >> read2.fna
cp ../../testdata/U89959_genomic.fas U89959.fna
./findemptyoutfiles.sh
./execcommand.pl tallymer.tex > tallymer-tmp.tex
# file output/gt-suffixerator--dna--pl--tis--suf--lcp--v--parts-4--db-read1.fna-read2.fna--indexname-reads.out already exists
# file output/gt-tallymer-occratio--output-unique-nonunique--minmersize-10--maxmersize-20--esa-reads.out already exists
# file output/gt-tallymer-occratio--output-unique-relative--minmersize-10--maxmersize-20--esa-reads.out already exists
# file output/gt-tallymer-occratio--output-unique-nonunique--mersizes-10-13-17--esa-reads.out already exists
# file output/gt-tallymer-mkindex--mersize-19--minocc-40--esa-reads.out already exists
# file output/gt-tallymer-mkindex--mersize-19--minocc-4--indexname-tyr-reads--counts--pl--esa-reads.out already exists
# file output/gt-tallymer-search--output-qseqnum-qpos-counts-sequence--tyr-tyr-reads--q-U89959.fna.out already exists
pdflatex tallymer-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
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entering extended mode
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.prj':
[2]

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[3]
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.prj':
[4] [5] [6] [7] [8] [9] (./tallymer-tmp.aux)

LaTeX Warning: There were undefined references.


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

 )
(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/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
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exmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw
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Output written on tallymer-tmp.pdf (9 pages, 139951 bytes).
Transcript written on tallymer-tmp.log.
pdflatex tallymer-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
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entering extended mode
(./tallymer-tmp.tex
LaTeX2e <2016/03/31> patch level 1
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.prj':
[2] [3]
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[]\OT1/pcr/m/n/12 gt tallymer occratio: error: fopen(): cannot open file 'reads
.prj':
[4] [5] [6] [7] [8] [9] (./tallymer-tmp.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/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
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Output written on tallymer-tmp.pdf (9 pages, 139318 bytes).
Transcript written on tallymer-tmp.log.
mv tallymer-tmp.pdf tallymer.pdf
../../bin/gt packedindex mkindex -dna -dir rev -parts 12 -bsize 10 \
                      -sprank -locfreq 32 -tis -ssp -indexname pck-human\
                      -db ../../testdata/at1MB
cp ../../testdata/Q1.gz Q1.gz
./findemptyoutfiles.sh
./execcommand.pl tagerator.tex > tagerator-tmp.tex
# file output/gt-tagerator--q-Q1.gz--maxocc-10--pck-pck-human.out already exists
# file output/gt-tagerator--q-Q1.gz--pck-pck-human--e-2.out already exists
# file output/gt-tagerator--q-Q1.gz--pck-pck-human--e-1--maxocc-5.out already exists
pdflatex tagerator-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
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entering extended mode
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ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
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Transcript written on tagerator-tmp.log.
pdflatex tagerator-tmp
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t 5 occurrences in the subject sequences[] 
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mv tagerator-tmp.pdf tagerator.pdf
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
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make[3]: [genomediff-pdf.aux] Error 1 (ignored)
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Transcript written on genomediff.log.
mv genomediff.aux genomediff-pdf.aux
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
bibtex genomediff
This is BibTeX, Version 0.99d (TeX Live 2016/Debian)
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Database file #1: gtmanuals.bib
test -e genomediff-pdf.bbl || touch genomediff-pdf.bbl
diff genomediff-pdf.bbl genomediff.bbl || mv genomediff.bbl genomediff-pdf.bbl && rm -f genomediff.bbl
0a1,25
> \begin{thebibliography}{1}
> 
> \bibitem{HAU:DOM:WIE:2008}
> Bernhard Haubold, Mirjana Domazet-Loso, and Thomas Wiehe.
> \newblock An alignment-free distance measure for closely related genomes.
> \newblock In {\em RECOMB-CG ’08: Proceedings of the international workshop on
>   Comparative Genomics}, pages 87--99, Berlin, Heidelberg, 2008.
>   Springer-Verlag.
> 
> \bibitem{HAU:PFA:DOM:WIE:2009}
> B.~Haubold, P.~Pfaffelhuber, M.~Domazet-Loso, and T.~Wiehe.
> \newblock Estimating mutation distances from unaligned genomes.
> \newblock {\em J. Comput. Biol.}, 16:1487--1500, "Oct" 2009.
> 
> \bibitem{HAU:REE:PFA:2011}
> Bernhard Haubold, Floyd~A. Reed, and Peter Pfaffelhuber.
> \newblock Alignment-free estimation of nucleotide diversity.
> \newblock {\em Bioinformatics}, 27(4):449--455, 2011.
> 
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
> 
> \end{thebibliography}
mv genomediff.aux genomediff-pdf.aux
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
test -e genomediff-pdf.bbl && mv genomediff-pdf.bbl genomediff.bbl
pdflatex genomediff.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genomediff.tex
LaTeX2e <2016/03/31> patch level 1
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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(/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/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/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/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(./genomediff.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd)

LaTeX Warning: Citation `HAU:DOM:WIE:2008' on page 1 undefined on input line 89
.


LaTeX Warning: Citation `HAU:PFA:DOM:WIE:2009' on page 1 undefined on input lin
e 89.


LaTeX Warning: Citation `HAU:REE:PFA:2011' on page 1 undefined on input line 89
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LaTeX Warning: Citation `genometools' on page 1 undefined on input line 97.

[1] [2] [3] [4]
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(./genomediff.bbl) [5] (./genomediff.aux)

LaTeX Warning: There were undefined references.


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

 )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176834 bytes).
Transcript written on genomediff.log.
pdflatex genomediff.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genomediff.tex
LaTeX2e <2016/03/31> patch level 1
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/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/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/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/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(./genomediff.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [1] [2] [3] [4]
Overfull \hbox (35.00766pt too wide) in paragraph at lines 323--324
[][][][][][][][][][][][][][][][][][][][][][][][] 
(./genomediff.bbl) [5] (./genomediff.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176600 bytes).
Transcript written on genomediff.log.
mv genomediff.aux genomediff-pdf.aux
test -e genomediff.bbl && mv genomediff.bbl genomediff-pdf.bbl
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds/doc/manuals'
make[2]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
bin/gt -test
seed=4015692188
Lua serializer module...ok
MD5 seqid module...ok
PBS finder module...ok
alignment class...ok
alphabet class...ok
array class...ok
array example...ok
array2dim example...ok
array2dim sparse example...ok
array3dim example...ok
basename module...ok
bit pack array class...ok
bit pack string module...ok
bittab class...ok
bittab example...ok
block class...ok
bsearch module...ok
codon iterator class, encoded...ok
codon iterator class, simple...ok
color space module...ok
combinatorics...ok
compactulongstore class...ok
compressed bitsequence...ok
countingsort module...ok
cstr module...ok
cstr table class...ok
database feature index class (GFF-like)...ok
description buffer class...ok
diagram class...ok
disc distri class...ok
dlist class...ok
dlist example...ok
dynamic bittab class...ok
editscript class...ok
element class...ok
elias gamma class...ok
encdesc class...ok
encseq builder class...ok
encseq gc module...ok
evaluator class...ok
feature in stream class...ok
feature node class...ok
feature node iterator example...ok
genome node class...ok
gff3 escaping module...ok
golomb class...ok
grep module...ok
hashmap class...ok
hashtable class...ok
hmm class...ok
huffman coding class...ok
imageinfo class...ok
interval tree class...ok
intset classes...ok
kmer_database class...ok
line class...ok
mathsupport module...ok
memory allocator module...ok
memory feature index class...ok
multieoplist...ok
popcount sorted tab...ok
priority queue class...ok
quality module...ok
queue class...ok
range class...ok
range minimum query class...ok
ranked list class...ok
rdj: string graph class...ok
rdj: suffix-prefix matches list module...ok
red-black tree class...ok
safearith example...ok
safearith module...ok
sequence buffer class...ok
splicedseq class...ok
splitter class...ok
string class...ok
string matching module...ok
style class...ok
symbol module...ok
tag value map class...ok
tag value map example...ok
tokenizer class...ok
track class...ok
translator class...ok
transtable class...ok
uint64hashtable...ok
xdrop...ok
cd testsuite; ./testsuite.rb -keywords 'gt_sketch and not gt_python and not gt_ruby' -threads 3
seed=1020893615
1378: gt sketch short test (unknown output format)                : ok
1377: gt sketch short test (stdin)                                : ok
1376: gt sketch short test                                        : ok
1379: gt sketch short test (unwriteable PNG file)                 : ok
1381: gt sketch short test (nonexistant style file)               : ok
1383: gt sketch prob 1                                            : ok
1382: gt sketch short test (invalid style file)                   : ok
1380: gt sketch short test (unwriteable PDF file)                 : ok
1384: gt sketch prob 2                                            : ok
1386: gt sketch multiline without parent                          : ok
1385: gt sketch track IDs to style file                           : ok
1387: gt sketch pipe                                              : ok
1389: gt sketch -showrecmaps                                      : ok
1390: gt sketch -showrecmaps (normal text size)                   : ok
1391: gt sketch -showrecmaps (narrow image)                       : ok
1392: gt sketch -showrecmaps (large text size)                    : ok
1393: gt sketch for transcript (neg. coords in ruler)             : ok
1395: sketch_constructed (C)                                      : ok
1396: sketch_parsed (C)                                           : ok
1397: sketch_parsed reverse order (C)                             : ok
1398: sketch_constructed (Lua)                                    : ok
1399: sketch_parsed (Lua)                                         : ok
1388: gt sketch streams <-> file output                           : ok
1394: gt sketch runtime Lua failures                              : ok
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
 fakeroot debian/rules binary-arch
dh binary-arch --with python2
   dh_testroot -a
   dh_prep -a
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
dh_auto_install -- installmanpages useshared=yes \
  x32=no 64bit=no errorcheck=no prefix=/<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr
	make -j1 install DESTDIR=/<<BUILDDIR>>/genometools-1.5.9\+ds/debian/tmp AM_UPDATE_INFO_DIR=no installmanpages useshared=yes x32=no 64bit=no errorcheck=no prefix=/<<BUILDDIR>>/genometools-1.5.9\+ds/debian/tmp/usr
make[2]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
[link libgenometools.so]
test -d /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/bin || mkdir -p /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/bin
cp bin/gt /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/bin
strip /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/bin/gt
cp -r gtdata /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/bin
test -d /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/core \
  || mkdir -p /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/core
cp src/core/*_api.h /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/core
test -d /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/extended \
          || mkdir -p /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/extended
cp src/extended/*_api.h /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/extended
test -d /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/annotationsketch \
          || mkdir -p /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/annotationsketch
cp src/annotationsketch/*_api.h \
          /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/annotationsketch
test -d /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/ltr \
          || mkdir -p /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/ltr
cp src/ltr/*_api.h /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools/ltr
cp obj/gt_config.h /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools
cp src/genometools.h /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include/genometools
test -d /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/lib || mkdir -p /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/lib
cp lib/libgenometools.a /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/lib
cp lib/libgenometools.so.0 /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/lib
ln -fs /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/lib/libgenometools.so.0 /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/lib/libgenometools.so
[build config script install]
sed -e 's!@CC@!cc!' -e 's!@CFLAGS@!-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security!' \
  -e 's!@CPPFLAGS@!-I\\"/<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/include\\" -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP -DHAVE_SQLITE!' \
  -e 's!@CXX@!g++!' -e 's!@CXXFLAGS@!-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security!' \
  -e 's!@LDFLAGS@!-L/<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/lib -fPIE -pie -Wl,-z,relro -Wl,-z,now -L/usr/local/lib!' \
  -e 's!@LIBS@! -lm -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lsqlite3!' -e "s!@VERSION@!`cat VERSION`!" \
  -e 's!@BUILDSTAMP@!"2016-07-29 13:10:32"!' \
  -e 's!@SYSTEM@!Linux!' <src/genometools-config.in \
  >/<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/bin/genometools-config
chmod 755 /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/bin/genometools-config
bin/gt -createman /tmp/gtmanpages
warning: skipping tool 'mgth' in iterator (not a GtTool object)
warning: skipping tool 'mkfmindex' in iterator (not a GtTool object)
warning: skipping tool 'suffixerator' in iterator (not a GtTool object)
warning: skipping tool 'chkintegrity' in iterator (not a GtTool object)
warning: skipping tool 'chksearch' in iterator (not a GtTool object)
warning: skipping tool 'mkctxmap' in iterator (not a GtTool object)
warning: skipping tool 'mkindex' in iterator (not a GtTool object)
warning: skipping tool 'trsuftab' in iterator (not a GtTool object)
test -d /<<BUILDDIR>>/genometools-1.5.9+ds/doc/manpages || mkdir -p /<<BUILDDIR>>/genometools-1.5.9+ds/doc/manpages
rm -f /<<BUILDDIR>>/genometools-1.5.9+ds/doc/manpages/*
scripts/create_manpages /tmp/gtmanpages /<<BUILDDIR>>/genometools-1.5.9+ds/doc/manpages
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs

test ! -d /<<BUILDDIR>>/genometools-1.5.9+ds/doc/manpages || \
  ((test -d /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/share/man/man1 || mkdir -p /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/share/man/man1) \
    && cp /<<BUILDDIR>>/genometools-1.5.9+ds/doc/manpages/* /<<BUILDDIR>>/genometools-1.5.9+ds/debian/tmp/usr/share/man/man1)
make[2]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
dh_auto_install --sourcedirectory=gtpython \
  --destdir=/<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
	python setup.py install --force --root=/<<BUILDDIR>>/genometools-1.5.9\+ds/debian/python-genometools --no-compile -O0 --install-layout=deb
running install
running build
running build_py
creating build
creating build/lib.linux-armv7l-2.7
creating build/lib.linux-armv7l-2.7/gt
copying gt/props.py -> build/lib.linux-armv7l-2.7/gt
copying gt/__init__.py -> build/lib.linux-armv7l-2.7/gt
copying gt/version.py -> build/lib.linux-armv7l-2.7/gt
copying gt/dlload.py -> build/lib.linux-armv7l-2.7/gt
creating build/lib.linux-armv7l-2.7/gt/core
copying gt/core/array.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/gtrange.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/alphabet.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/gtstr.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/warning.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/str_array.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/encseq.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/__init__.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/error.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/readmode.py -> build/lib.linux-armv7l-2.7/gt/core
creating build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/color.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/custom_track.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/feature_stream.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/diagram.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/graphics.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/canvas.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/custom_track_example.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/__init__.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/layout.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/feature_index.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/image_info.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/block.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/style.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/rec_map.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
creating build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/region_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/sequence_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/anno_db.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/sort_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/eof_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/genome_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/merge_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/meta_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/strand.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_out_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/add_introns_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_in_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/dup_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_visitor_example.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/rdb.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/__init__.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/genome_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_index.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_stream_example.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/inter_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/comment_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/node_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
running install_lib
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/props.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/__init__.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/version.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/dlload.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/array.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtrange.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/alphabet.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtstr.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/warning.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/str_array.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/encseq.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/__init__.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/error.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/readmode.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/color.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/diagram.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/graphics.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/canvas.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track_example.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/__init__.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/layout.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_index.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/image_info.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/block.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/style.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/rec_map.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
creating /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_visitor.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/region_node.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/sequence_node.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/anno_db.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/sort_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/eof_node.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_node.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/merge_feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/meta_node.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/strand.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_out_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/add_introns_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_in_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/dup_feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor_example.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/rdb.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/__init__.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_node.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_index.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream_example.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/inter_feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/comment_node.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/node_visitor.py -> /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
running install_egg_info
Writing /<<BUILDDIR>>/genometools-1.5.9+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/GenomeTools-1.5.9.egg-info
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
   dh_install -a
   dh_installdocs -a
   dh_installchangelogs -a
   dh_installman -a
   dh_python2 -a
E: dh_python2 dh_python2:396: no package to act on (python-foo or one with ${python:Depends} in Depends)
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   debian/rules override_dh_strip
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
dh_strip --dbg-package=genometools-dbg
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.9+ds'
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libdl.so.2 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libglib-2.0.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against libglib-2.0.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-des56.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-lpeg.so.2 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-filesystem.so.0 (it uses none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package libgenometools0-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package genometools-dbg: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'genometools' in '../genometools_1.5.9+ds-2_armhf.deb'.
dpkg-deb: building package 'libgenometools0' in '../libgenometools0_1.5.9+ds-2_armhf.deb'.
dpkg-deb: building package 'genometools-dbg' in '../genometools-dbg_1.5.9+ds-2_armhf.deb'.
dpkg-deb: building package 'libgenometools0-dev' in '../libgenometools0-dev_1.5.9+ds-2_armhf.deb'.
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../genometools_1.5.9+ds-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build genometools-1.5.9+ds
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160729-1345

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


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


genometools_1.5.9+ds-2_armhf.changes:
-------------------------------------

Format: 1.8
Date: Sat, 23 Jul 2016 10:54:26 +0000
Source: genometools
Binary: genometools genometools-common libgenometools0 libgenometools0-dev genometools-doc genometools-dbg python-genometools
Architecture: armhf
Version: 1.5.9+ds-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
 genometools - versatile genome analysis toolkit
 genometools-common - shared data files for GenomeTools
 genometools-dbg - versatile genome analysis toolkit, with debug symbols
 genometools-doc - documentation for GenomeTools
 libgenometools0 - versatile genome analysis library
 libgenometools0-dev - development files for GenomeTools
 python-genometools - Python bindings for genometools
Changes:
 genometools (1.5.9+ds-2) unstable; urgency=medium
 .
   * Use fixed date in split manual source.
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Files:
 623fe5bd927add749f9e964330912b82 4143488 debug extra genometools-dbg_1.5.9+ds-2_armhf.deb
 0a6d90f23f7244afcb3c3b68ef952f65 1731292 science optional genometools_1.5.9+ds-2_armhf.deb
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 fa68d10f1dd7d336425bec15425fc8af 1604576 libs optional libgenometools0_1.5.9+ds-2_armhf.deb

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


genometools-dbg_1.5.9+ds-2_armhf.deb
------------------------------------

 new debian package, version 2.0.
 size 4143488 bytes: control archive=715 bytes.
     632 bytes,    15 lines      control              
     341 bytes,     4 lines      md5sums              
 Package: genometools-dbg
 Source: genometools
 Version: 1.5.9+ds-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4615
 Depends: genometools (= 1.5.9+ds-2) | libgenometools0 (= 1.5.9+ds-2)
 Section: debug
 Priority: extra
 Homepage: http://genometools.org
 Description: versatile genome analysis toolkit, with debug symbols
  This package contains debug information stripped from the GenomeTools.
  You may decide to install it to help identifying issues, typically
  to help communication with upstream developers.
 Build-Ids: 02c76ae09b1f9b30a167e92f5dcd969a74d867b2

drwxr-xr-x root/root         0 2016-07-29 13:44 ./
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/lib/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/lib/debug/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/lib/debug/.build-id/02/
-rw-r--r-- root/root   4699184 2016-07-29 13:43 ./usr/lib/debug/.build-id/02/c76ae09b1f9b30a167e92f5dcd969a74d867b2.debug
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/doc/genometools-dbg/
-rw-r--r-- root/root      2967 2016-07-23 10:54 ./usr/share/doc/genometools-dbg/changelog.Debian.gz
-rw-r--r-- root/root      6265 2016-07-21 12:32 ./usr/share/doc/genometools-dbg/changelog.gz
-rw-r--r-- root/root      5106 2016-03-11 09:51 ./usr/share/doc/genometools-dbg/copyright


genometools_1.5.9+ds-2_armhf.deb
--------------------------------

 new debian package, version 2.0.
 size 1731292 bytes: control archive=3563 bytes.
     890 bytes,    16 lines      control              
    7249 bytes,   101 lines      md5sums              
 Package: genometools
 Version: 1.5.9+ds-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5534
 Depends: libbz2-1.0, libc6 (>= 2.15), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libglib2.0-0 (>= 2.12.0), liblua5.1-0, libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libsqlite3-0 (>= 3.5.9), libtre5, lua-filesystem, lua-lpeg, lua-md5, zlib1g (>= 1:1.2.3.3), genometools-common
 Section: science
 Priority: optional
 Homepage: http://genometools.org
 Description: versatile genome analysis toolkit
  The GenomeTools contains a collection of useful tools for biological
  sequence analysis and -presentation combined into a single binary.
  .
  The toolkit contains binaries for sequence and annotation handling, sequence
  compression, index structure generation and access, annotation visualization,
  and much more.

drwxr-xr-x root/root         0 2016-07-29 13:44 ./
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/bin/
-rwxr-xr-x root/root   5498540 2016-07-29 13:43 ./usr/bin/gt
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/doc/genometools/
-rw-r--r-- root/root       833 2016-07-21 12:32 ./usr/share/doc/genometools/CONTRIBUTORS
-rw-r--r-- root/root      1772 2016-07-21 12:32 ./usr/share/doc/genometools/README
-rw-r--r-- root/root         6 2016-07-21 12:32 ./usr/share/doc/genometools/VERSION
-rw-r--r-- root/root      2967 2016-07-23 10:54 ./usr/share/doc/genometools/changelog.Debian.gz
-rw-r--r-- root/root      6265 2016-07-21 12:32 ./usr/share/doc/genometools/changelog.gz
-rw-r--r-- root/root      5106 2016-03-11 09:51 ./usr/share/doc/genometools/copyright
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/man/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/man/man1/
-rw-r--r-- root/root       835 2016-07-29 13:43 ./usr/share/man/man1/gt-bed_to_gff3.1.gz
-rw-r--r-- root/root      1622 2016-07-29 13:43 ./usr/share/man/man1/gt-cds.1.gz
-rw-r--r-- root/root      1249 2016-07-29 13:43 ./usr/share/man/man1/gt-chain2dim.1.gz
-rw-r--r-- root/root      1071 2016-07-29 13:43 ./usr/share/man/man1/gt-chseqids.1.gz
-rw-r--r-- root/root       667 2016-07-29 13:43 ./usr/share/man/man1/gt-clean.1.gz
-rw-r--r-- root/root      1036 2016-07-29 13:43 ./usr/share/man/man1/gt-compreads-compress.1.gz
-rw-r--r-- root/root      1009 2016-07-29 13:43 ./usr/share/man/man1/gt-compreads-decompress.1.gz
-rw-r--r-- root/root      1079 2016-07-29 13:43 ./usr/share/man/man1/gt-compreads-refcompress.1.gz
-rw-r--r-- root/root       876 2016-07-29 13:43 ./usr/share/man/man1/gt-compreads-refdecompress.1.gz
-rw-r--r-- root/root       738 2016-07-29 13:43 ./usr/share/man/man1/gt-compreads.1.gz
-rw-r--r-- root/root       771 2016-07-29 13:43 ./usr/share/man/man1/gt-condenseq.1.gz
-rw-r--r-- root/root       775 2016-07-29 13:43 ./usr/share/man/man1/gt-congruence-spacedseed.1.gz
-rw-r--r-- root/root       790 2016-07-29 13:43 ./usr/share/man/man1/gt-congruence.1.gz
-rw-r--r-- root/root       969 2016-07-29 13:43 ./usr/share/man/man1/gt-convertseq.1.gz
-rw-r--r-- root/root      1412 2016-07-29 13:43 ./usr/share/man/man1/gt-csa.1.gz
-rw-r--r-- root/root       648 2016-07-29 13:43 ./usr/share/man/man1/gt-dot.1.gz
-rw-r--r-- root/root       813 2016-07-29 13:43 ./usr/share/man/man1/gt-dupfeat.1.gz
-rw-r--r-- root/root       790 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq-bench.1.gz
-rw-r--r-- root/root       840 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq-bitextract.1.gz
-rw-r--r-- root/root       824 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq-check.1.gz
-rw-r--r-- root/root      1052 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq-decode.1.gz
-rw-r--r-- root/root      1069 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq-encode.1.gz
-rw-r--r-- root/root       939 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq-info.1.gz
-rw-r--r-- root/root       801 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq-md5.1.gz
-rw-r--r-- root/root      1029 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq-sample.1.gz
-rw-r--r-- root/root       784 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq.1.gz
-rw-r--r-- root/root       913 2016-07-29 13:43 ./usr/share/man/man1/gt-encseq2spm.1.gz
-rw-r--r-- root/root      1174 2016-07-29 13:43 ./usr/share/man/man1/gt-eval.1.gz
-rw-r--r-- root/root      2045 2016-07-29 13:43 ./usr/share/man/man1/gt-extractfeat.1.gz
-rw-r--r-- root/root      2122 2016-07-29 13:43 ./usr/share/man/man1/gt-extractseq.1.gz
-rw-r--r-- root/root       804 2016-07-29 13:43 ./usr/share/man/man1/gt-fastq_sample.1.gz
-rw-r--r-- root/root       869 2016-07-29 13:43 ./usr/share/man/man1/gt-featureindex.1.gz
-rw-r--r-- root/root      1584 2016-07-29 13:43 ./usr/share/man/man1/gt-fingerprint.1.gz
-rw-r--r-- root/root      1712 2016-07-29 13:43 ./usr/share/man/man1/gt-genomediff.1.gz
-rw-r--r-- root/root      1923 2016-07-29 13:43 ./usr/share/man/man1/gt-gff3.1.gz
-rw-r--r-- root/root       776 2016-07-29 13:43 ./usr/share/man/man1/gt-gff3_to_gtf.1.gz
-rw-r--r-- root/root       992 2016-07-29 13:43 ./usr/share/man/man1/gt-gff3validator.1.gz
-rw-r--r-- root/root       803 2016-07-29 13:43 ./usr/share/man/man1/gt-gtf_to_gff3.1.gz
-rw-r--r-- root/root      2418 2016-07-29 13:43 ./usr/share/man/man1/gt-hop.1.gz
-rw-r--r-- root/root      1528 2016-07-29 13:43 ./usr/share/man/man1/gt-id_to_md5.1.gz
-rw-r--r-- root/root      1145 2016-07-29 13:43 ./usr/share/man/man1/gt-inlineseq_add.1.gz
-rw-r--r-- root/root       760 2016-07-29 13:43 ./usr/share/man/man1/gt-inlineseq_split.1.gz
-rw-r--r-- root/root       828 2016-07-29 13:43 ./usr/share/man/man1/gt-interfeat.1.gz
-rw-r--r-- root/root       665 2016-07-29 13:43 ./usr/share/man/man1/gt-loccheck.1.gz
-rw-r--r-- root/root       877 2016-07-29 13:43 ./usr/share/man/man1/gt-ltrclustering.1.gz
-rw-r--r-- root/root      2165 2016-07-29 13:43 ./usr/share/man/man1/gt-ltrdigest.1.gz
-rw-r--r-- root/root      1564 2016-07-29 13:43 ./usr/share/man/man1/gt-ltrharvest.1.gz
-rw-r--r-- root/root       939 2016-07-29 13:43 ./usr/share/man/man1/gt-matchtool.1.gz
-rw-r--r-- root/root       892 2016-07-29 13:43 ./usr/share/man/man1/gt-matstat.1.gz
-rw-r--r-- root/root       831 2016-07-29 13:43 ./usr/share/man/man1/gt-md5_to_id.1.gz
-rw-r--r-- root/root       886 2016-07-29 13:43 ./usr/share/man/man1/gt-merge.1.gz
-rw-r--r-- root/root       802 2016-07-29 13:43 ./usr/share/man/man1/gt-mergefeat.1.gz
-rw-r--r-- root/root       843 2016-07-29 13:43 ./usr/share/man/man1/gt-mkfeatureindex.1.gz
-rw-r--r-- root/root       666 2016-07-29 13:43 ./usr/share/man/man1/gt-mmapandread.1.gz
-rw-r--r-- root/root      1294 2016-07-29 13:43 ./usr/share/man/man1/gt-orffinder.1.gz
-rw-r--r-- root/root       832 2016-07-29 13:43 ./usr/share/man/man1/gt-packedindex.1.gz
-rw-r--r-- root/root       742 2016-07-29 13:43 ./usr/share/man/man1/gt-prebwt.1.gz
-rw-r--r-- root/root      1071 2016-07-29 13:43 ./usr/share/man/man1/gt-readjoiner-assembly.1.gz
-rw-r--r-- root/root       910 2016-07-29 13:43 ./usr/share/man/man1/gt-readjoiner-overlap.1.gz
-rw-r--r-- root/root      1256 2016-07-29 13:43 ./usr/share/man/man1/gt-readjoiner-prefilter.1.gz
-rw-r--r-- root/root       850 2016-07-29 13:43 ./usr/share/man/man1/gt-readjoiner.1.gz
-rw-r--r-- root/root      1163 2016-07-29 13:43 ./usr/share/man/man1/gt-repfind.1.gz
-rw-r--r-- root/root       757 2016-07-29 13:43 ./usr/share/man/man1/gt-scriptfilter.1.gz
-rw-r--r-- root/root      1314 2016-07-29 13:43 ./usr/share/man/man1/gt-seed_extend.1.gz
-rw-r--r-- root/root      1835 2016-07-29 13:43 ./usr/share/man/man1/gt-select.1.gz
-rw-r--r-- root/root      1094 2016-07-29 13:43 ./usr/share/man/man1/gt-seq.1.gz
-rw-r--r-- root/root       998 2016-07-29 13:43 ./usr/share/man/man1/gt-seqfilter.1.gz
-rw-r--r-- root/root       652 2016-07-29 13:43 ./usr/share/man/man1/gt-seqids.1.gz
-rw-r--r-- root/root      1173 2016-07-29 13:43 ./usr/share/man/man1/gt-seqmutate.1.gz
-rw-r--r-- root/root       821 2016-07-29 13:43 ./usr/share/man/man1/gt-seqorder.1.gz
-rw-r--r-- root/root       895 2016-07-29 13:43 ./usr/share/man/man1/gt-seqstat.1.gz
-rw-r--r-- root/root       894 2016-07-29 13:43 ./usr/share/man/man1/gt-seqtransform.1.gz
-rw-r--r-- root/root       853 2016-07-29 13:43 ./usr/share/man/man1/gt-seqtranslate.1.gz
-rw-r--r-- root/root       945 2016-07-29 13:43 ./usr/share/man/man1/gt-sequniq.1.gz
-rw-r--r-- root/root      1429 2016-07-29 13:43 ./usr/share/man/man1/gt-shredder.1.gz
-rw-r--r-- root/root       773 2016-07-29 13:43 ./usr/share/man/man1/gt-shulengthdist.1.gz
-rw-r--r-- root/root      1021 2016-07-29 13:43 ./usr/share/man/man1/gt-simreads.1.gz
-rw-r--r-- root/root      1093 2016-07-29 13:43 ./usr/share/man/man1/gt-sketch.1.gz
-rw-r--r-- root/root      1028 2016-07-29 13:43 ./usr/share/man/man1/gt-sketch_page.1.gz
-rw-r--r-- root/root      1950 2016-07-29 13:43 ./usr/share/man/man1/gt-snpper.1.gz
-rw-r--r-- root/root      1549 2016-07-29 13:43 ./usr/share/man/man1/gt-speck.1.gz
-rw-r--r-- root/root      1528 2016-07-29 13:43 ./usr/share/man/man1/gt-splicesiteinfo.1.gz
-rw-r--r-- root/root       862 2016-07-29 13:43 ./usr/share/man/man1/gt-splitfasta.1.gz
-rw-r--r-- root/root       972 2016-07-29 13:43 ./usr/share/man/man1/gt-stat.1.gz
-rw-r--r-- root/root      1250 2016-07-29 13:43 ./usr/share/man/man1/gt-tagerator.1.gz
-rw-r--r-- root/root      1038 2016-07-29 13:43 ./usr/share/man/man1/gt-tallymer-mkindex.1.gz
-rw-r--r-- root/root      1014 2016-07-29 13:43 ./usr/share/man/man1/gt-tallymer-occratio.1.gz
-rw-r--r-- root/root       904 2016-07-29 13:43 ./usr/share/man/man1/gt-tallymer-search.1.gz
-rw-r--r-- root/root       803 2016-07-29 13:43 ./usr/share/man/man1/gt-tallymer.1.gz
-rw-r--r-- root/root      1519 2016-07-29 13:43 ./usr/share/man/man1/gt-tirvish.1.gz
-rw-r--r-- root/root      1150 2016-07-29 13:43 ./usr/share/man/man1/gt-uniq.1.gz
-rw-r--r-- root/root       892 2016-07-29 13:43 ./usr/share/man/man1/gt-uniquesub.1.gz
-rw-r--r-- root/root       728 2016-07-29 13:43 ./usr/share/man/man1/gt-wtree.1.gz
-rw-r--r-- root/root      1616 2016-07-29 13:43 ./usr/share/man/man1/gt.1.gz


libgenometools0-dev_1.5.9+ds-2_armhf.deb
----------------------------------------

 new debian package, version 2.0.
 size 78182 bytes: control archive=5117 bytes.
     678 bytes,    18 lines      control              
   13509 bytes,   160 lines      md5sums              
 Package: libgenometools0-dev
 Source: genometools
 Version: 1.5.9+ds-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 561
 Depends: libgenometools0 (= 1.5.9+ds-2)
 Section: libdevel
 Priority: optional
 Homepage: http://genometools.org
 Description: development files for GenomeTools
  This package contains the GenomeTools static library and necessary
  header files.
  .
  Besides basic bioinformatics data structures, the library contains components
  for sequence and annotation handling, sequence compression, index structure
  generation and access, efficient matching, annotation visualization and much
  more.

drwxr-xr-x root/root         0 2016-07-29 13:44 ./
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/
drwxr-xr-x root/root         0 2016-07-29 13:10 ./usr/include/
drwxr-xr-x root/root         0 2016-07-29 13:10 ./usr/include/genometools/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/include/genometools/annotationsketch/
-rw-r--r-- root/root      3569 2016-07-29 13:10 ./usr/include/genometools/annotationsketch/block_api.h
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drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/lib/
lrwxrwxrwx root/root         0 2016-07-29 13:43 ./usr/lib/libgenometools.so -> libgenometools.so.0
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/doc/libgenometools0-dev/
-rw-r--r-- root/root      2967 2016-07-23 10:54 ./usr/share/doc/libgenometools0-dev/changelog.Debian.gz
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-rw-r--r-- root/root      5106 2016-03-11 09:51 ./usr/share/doc/libgenometools0-dev/copyright


libgenometools0_1.5.9+ds-2_armhf.deb
------------------------------------

 new debian package, version 2.0.
 size 1604576 bytes: control archive=967 bytes.
    1009 bytes,    19 lines      control              
     297 bytes,     4 lines      md5sums              
      33 bytes,     1 lines      shlibs               
      60 bytes,     2 lines      triggers             
 Package: libgenometools0
 Source: genometools
 Version: 1.5.9+ds-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5374
 Depends: libbz2-1.0, libc6 (>= 2.15), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libglib2.0-0 (>= 2.12.0), liblua5.1-0, libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libsqlite3-0 (>= 3.5.9), libtre5, lua-filesystem, lua-lpeg, lua-md5, zlib1g (>= 1:1.2.3.3), genometools-common
 Section: libs
 Priority: optional
 Homepage: http://genometools.org
 Description: versatile genome analysis library
  This package contains the GenomeTools shared library and header
  files. It offers efficient sequence analysis components, available
  via an object-oriented interface.
  .
  Besides basic bioinformatics data structures, the library contains components
  for sequence and annotation handling, sequence compression, index structure
  generation and access, efficient matching, annotation visualization and much
  more.

drwxr-xr-x root/root         0 2016-07-29 13:44 ./
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/lib/
-rw-r--r-- root/root   5477648 2016-07-29 13:43 ./usr/lib/libgenometools.so.0
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-07-29 13:43 ./usr/share/doc/libgenometools0/
-rw-r--r-- root/root      2967 2016-07-23 10:54 ./usr/share/doc/libgenometools0/changelog.Debian.gz
-rw-r--r-- root/root      6265 2016-07-21 12:32 ./usr/share/doc/libgenometools0/changelog.gz
-rw-r--r-- root/root      5106 2016-03-11 09:51 ./usr/share/doc/libgenometools0/copyright


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


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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

Build Architecture: armhf
Build-Space: 255124
Build-Time: 4773
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 2934
Job: genometools_1.5.9+ds-2
Machine Architecture: armhf
Package: genometools
Package-Time: 7852
Source-Version: 1.5.9+ds-2
Space: 255124
Status: successful
Version: 1.5.9+ds-2
--------------------------------------------------------------------------------
Finished at 20160729-1345
Build needed 02:10:52, 255124k disc space

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