sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build02.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ velvet 1.2.03~nozlibcopy-1 (armhf) 04 May 2012 23:16 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: velvet Version: 1.2.03~nozlibcopy-1 Source Version: 1.2.03~nozlibcopy-1 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/velvet-G_es2A/velvet-1.2.03~nozlibcopy' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/velvet-G_es2A' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-5d4d7e57-79c9-40d6-8a33-64927aee5e04' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'velvet' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/velvet/trunk/ Need to get 3994 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main velvet 1.2.03~nozlibcopy-1 (dsc) [2177 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main velvet 1.2.03~nozlibcopy-1 (tar) [3982 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main velvet 1.2.03~nozlibcopy-1 (diff) [8940 B] Fetched 3994 kB in 0s (9588 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-0daikV/apt_archive/sbuild-build-depends-core-dummy.deb'. OK 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 debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10678 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), zlib1g-dev, help2man, quilt, texlive-latex-base Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), zlib1g-dev, help2man, quilt, texlive-latex-base dpkg-deb: building package `sbuild-build-depends-velvet-dummy' in `/«BUILDDIR»/resolver-OS6sf3/apt_archive/sbuild-build-depends-velvet-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install velvet build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper diffstat ed file fontconfig-config gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libexpat1 libffi5 libfontconfig1 libfreetype6 libglib2.0-0 libice6 libjpeg8 libkpathsea5 liblcms1 libmagic1 libopenjpeg2 libpaper-utils libpaper1 libpcre3 libpipeline1 libpng12-0 libpoppler13 libsm6 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxt6 luatex man-db mime-support po-debconf quilt tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-base ttf-dejavu-core x11-common zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff liblcms-utils less www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent perl-tk ghostscript xpdf-reader pdf-viewer gv postscript-viewer Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info poppler-data xml-core texlive-luatex libmail-sendmail-perl lmodern texlive-latex-base-doc The following NEW packages will be installed: bsdmainutils debhelper diffstat ed file fontconfig-config gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libexpat1 libffi5 libfontconfig1 libfreetype6 libglib2.0-0 libice6 libjpeg8 libkpathsea5 liblcms1 libmagic1 libopenjpeg2 libpaper-utils libpaper1 libpcre3 libpipeline1 libpng12-0 libpoppler13 libsm6 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxt6 luatex man-db mime-support po-debconf quilt sbuild-build-depends-velvet-dummy tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-base ttf-dejavu-core x11-common zlib1g-dev 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 94.8 kB/44.6 MB of archives. After this operation, 99.1 MB of additional disk space will be used. Get:1 http://repo.raspbian.lan/raspbian/ testing/main help2man armhf 1.40.9 [94.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 94.8 kB in 0s (2107 kB/s) Selecting previously unselected package libpcre3:armhf. (Reading database ... 10678 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-4_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9_armhf.deb) ... Selecting previously unselected package libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.0-4_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libexpat1:armhf. Unpacking libexpat1:armhf (from .../libexpat1_2.1.0-1_armhf.deb) ... Selecting previously unselected package libfreetype6:armhf. Unpacking libfreetype6:armhf (from .../libfreetype6_2.4.9-1_armhf.deb) ... Selecting previously unselected package ttf-dejavu-core. Unpacking ttf-dejavu-core (from .../ttf-dejavu-core_2.33-2_all.deb) ... Selecting previously unselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.8.0-3.1_all.deb) ... Selecting previously unselected package libfontconfig1:armhf. Unpacking libfontconfig1:armhf (from .../libfontconfig1_2.8.0-3.1_armhf.deb) ... Selecting previously unselected package x11-common. Unpacking x11-common (from .../x11-common_1%3a7.6+12_all.deb) ... Selecting previously unselected package libice6:armhf. Unpacking libice6:armhf (from .../libice6_2%3a1.0.8-2_armhf.deb) ... Selecting previously unselected package libjpeg8:armhf. Unpacking libjpeg8:armhf (from .../libjpeg8_8d-1_armhf.deb) ... Selecting previously unselected package libpng12-0:armhf. Unpacking libpng12-0:armhf (from .../libpng12-0_1.2.49-1_armhf.deb) ... Selecting previously unselected package libsm6:armhf. Unpacking libsm6:armhf (from .../libsm6_2%3a1.2.1-2_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package libxau6:armhf. Unpacking libxau6:armhf (from .../libxau6_1%3a1.0.7-1_armhf.deb) ... 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Selecting previously unselected package libxaw7:armhf. Unpacking libxaw7:armhf (from .../libxaw7_2%3a1.0.10-2_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120419_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-2_armhf.deb) ... Selecting previously unselected package ed. Unpacking ed (from .../archives/ed_1.6-1_armhf.deb) ... Selecting previously unselected package help2man. Unpacking help2man (from .../help2man_1.40.9_armhf.deb) ... Selecting previously unselected package libkpathsea5. Unpacking libkpathsea5 (from .../libkpathsea5_2009-12_armhf.deb) ... Selecting previously unselected package liblcms1. Unpacking liblcms1 (from .../liblcms1_1.19.dfsg-1_armhf.deb) ... Selecting previously unselected package libpaper1. Unpacking libpaper1 (from .../libpaper1_1.1.24+nmu1_armhf.deb) ... Selecting previously unselected package libpaper-utils. Unpacking libpaper-utils (from .../libpaper-utils_1.1.24+nmu1_armhf.deb) ... Selecting previously unselected package libopenjpeg2. Unpacking libopenjpeg2 (from .../libopenjpeg2_1.3+dfsg-4_armhf.deb) ... Selecting previously unselected package libpoppler13. Unpacking libpoppler13 (from .../libpoppler13_0.16.7-3_armhf.deb) ... Selecting previously unselected package luatex. Unpacking luatex (from .../luatex_0.70.1-3_armhf.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ... Selecting previously unselected package tex-common. Unpacking tex-common (from .../tex-common_2.10_all.deb) ... Selecting previously unselected package texlive-common. Unpacking texlive-common (from .../texlive-common_2009-15_all.deb) ... Selecting previously unselected package texlive-doc-base. Unpacking texlive-doc-base (from .../texlive-doc-base_2009-2_all.deb) ... Selecting previously unselected package texlive-binaries. Unpacking texlive-binaries (from .../texlive-binaries_2009-12_armhf.deb) ... Selecting previously unselected package texlive-base. Unpacking texlive-base (from .../texlive-base_2009-15_all.deb) ... Selecting previously unselected package texlive-latex-base. Unpacking texlive-latex-base (from .../texlive-latex-base_2009-15_all.deb) ... Selecting previously unselected package zlib1g-dev:armhf. Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-velvet-dummy. Unpacking sbuild-build-depends-velvet-dummy (from .../sbuild-build-depends-velvet-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-4) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.0-4) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libexpat1:armhf (2.1.0-1) ... Setting up libfreetype6:armhf (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.8.0-3.1) ... Setting up libfontconfig1:armhf (2.8.0-3.1) ... Setting up x11-common (1:7.6+12) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:armhf (2:1.0.8-2) ... Setting up libjpeg8:armhf (8d-1) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libsm6:armhf (2:1.2.1-2) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-1) ... Setting up libx11-data (2:1.4.4-4) ... Setting up libx11-6:armhf (2:1.4.4-4) ... Setting up libxext6:armhf (2:1.3.1-2) ... Setting up libxt6:armhf (1:1.1.3-1) ... Setting up libxmu6:armhf (2:1.1.1-1) ... Setting up libxpm4:armhf (1:3.5.10-1) ... Setting up libxaw7:armhf (2:1.0.10-2) ... Setting up bsdmainutils (9.0.1) ... 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. Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up diffstat (1.55-2) ... Setting up ed (1.6-1) ... Setting up help2man (1.40.9) ... Setting up libkpathsea5 (2009-12) ... Setting up liblcms1 (1.19.dfsg-1) ... Setting up libpaper1 (1.1.24+nmu1) ... Creating config file /etc/papersize with new version Setting up libpaper-utils (1.1.24+nmu1) ... Setting up libopenjpeg2 (1.3+dfsg-4) ... Setting up libpoppler13 (0.16.7-3) ... Setting up luatex (0.70.1-3) ... texlive-base is not ready, cannot create formats Setting up quilt (0.60-2) ... Setting up tex-common (2.10) ... Creating config file /etc/texmf/texmf.d/05TeXMF.cnf with new version Creating config file /etc/texmf/texmf.d/15Plain.cnf with new version Creating config file /etc/texmf/texmf.d/45TeXinputs.cnf with new version Creating config file /etc/texmf/texmf.d/55Fonts.cnf with new version Creating config file /etc/texmf/texmf.d/65BibTeX.cnf with new version Creating config file /etc/texmf/texmf.d/75DviPS.cnf with new version Creating config file /etc/texmf/texmf.d/80DVIPDFMx.cnf with new version Creating config file /etc/texmf/texmf.d/85Misc.cnf with new version Creating config file /etc/texmf/texmf.d/90TeXDoc.cnf with new version Creating config file /etc/texmf/texmf.d/95NonPath.cnf with new version Creating config file /etc/texmf/updmap.d/00updmap.cfg with new version Creating config file /etc/texmf/texmf.cnf with new version Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up texlive-common (2009-15) ... Setting up texlive-doc-base (2009-2) ... Setting up texlive-binaries (2009-12) ... 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. Building format(s) --refresh. This may take some time... done. Setting up zlib1g-dev:armhf (1:1.2.6.dfsg-2) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2009-15) ... Creating config file /etc/texmf/dvips/config/config.ps with new version Creating config file /etc/texmf/tex/generic/config/pdftexconfig.tex with new version Creating config file /etc/texmf/dvipdfmx/dvipdfmx.cfg with new version Creating config file /etc/texmf/xdvi/XDvi with new version Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building e-tex based formats --byhyphen /var/lib/texmf/tex/generic/config/language.def. This may take some time... done. Setting up texlive-latex-base (2009-15) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up sbuild-build-depends-velvet-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-30 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffstat_1.55-2 diffutils_1:3.2-2 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 ed_1.6-1 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 fontconfig-config_2.8.0-3.1 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 help2man_1.40.9 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-30 libc-dev-bin_2.13-30 libc6_2.13-30 libc6-dev_2.13-30 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libfontconfig1_2.8.0-3.1 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libglib2.0-0_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi libice6_2:1.0.8-2 libjpeg8_8d-1 libkpathsea5_2009-12 liblcms1_1.19.dfsg-1 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-6 libncursesw5_5.9-6 libopenjpeg2_1.3+dfsg-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_1:8.30-4 libpipeline1_1.2.1-1 libpng12-0_1.2.49-1 libpoppler13_0.16.7-3 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsm6_2:1.2.1-2 libss2_1.42.2-2 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libx11-6_2:1.4.4-4 libx11-data_2:1.4.4-4 libxau6_1:1.0.7-1 libxaw7_2:1.0.10-2 libxcb1_1.8.1-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.1-2 libxml2_2.7.8.dfsg-9 libxmu6_2:1.1.1-1 libxpm4_1:3.5.10-1 libxt6_1:1.1.3-1 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 luatex_0.70.1-3 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-6 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-velvet-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tex-common_2.10 texlive-base_2009-15 texlive-binaries_2009-12 texlive-common_2009-15 texlive-doc-base_2009-2 texlive-latex-base_2009-15 ttf-dejavu-core_2.33-2 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 x11-common_1:7.6+12 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Feb 16 04:39:43 2012 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./velvet_1.2.03~nozlibcopy-1.dsc dpkg-source: info: extracting velvet in velvet-1.2.03~nozlibcopy dpkg-source: info: unpacking velvet_1.2.03~nozlibcopy.orig.tar.xz dpkg-source: info: unpacking velvet_1.2.03~nozlibcopy-1.debian.tar.gz dpkg-source: info: applying include_debians_zlib.patch dpkg-source: info: applying shuffleSequences_fasta.patch dpkg-source: info: applying fix-perl-path.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-5d4d7e57-79c9-40d6-8a33-64927aee5e04 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package velvet dpkg-buildpackage: source version 1.2.03~nozlibcopy-1 dpkg-source --before-build velvet-1.2.03~nozlibcopy dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean --with quilt dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_clean make[2]: Entering directory `/«PKGBUILDDIR»' rm obj/*.o obj/dbg/*.o ./velvet* rm: cannot remove `obj/*.o': No such file or directory rm: cannot remove `obj/dbg/*.o': No such file or directory rm: cannot remove `./velvet*': No such file or directory make[2]: [clean] Error 1 (ignored) rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log make[2]: Leaving directory `/«PKGBUILDDIR»' rm -rf zlib make[1]: Leaving directory `/«PKGBUILDDIR»' dh_quilt_unpatch Removing patch fix-perl-path.patch Restoring contrib/select_paired/select_paired.pl Removing patch shuffleSequences_fasta.patch Restoring contrib/shuffleSequences_fasta/shuffleSequences_fasta.py Removing patch include_debians_zlib.patch Restoring src/binarySequences.c Restoring src/readSet.c No patches applied dh_clean debian/rules build-arch dh build-arch --with quilt dh_testdir -a dh_quilt_patch -a Applying patch include_debians_zlib.patch patching file src/readSet.c Hunk #1 succeeded at 37 (offset 2 lines). patching file src/binarySequences.c Applying patch shuffleSequences_fasta.patch patching file contrib/shuffleSequences_fasta/shuffleSequences_fasta.py Applying patch fix-perl-path.patch patching file contrib/select_paired/select_paired.pl Now at patch fix-perl-path.patch dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' touch zlib # prevents the zlib in the ‘third-party’ folder to be built. dh_auto_build -- OPENMP=1 make[2]: Entering directory `/«PKGBUILDDIR»' rm obj/*.o obj/dbg/*.o rm: cannot remove `obj/*.o': No such file or directory rm: cannot remove `obj/dbg/*.o': No such file or directory make[2]: [cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1060:14: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:3: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:245:3: warning: case label value is less than minimum value for type [enabled by default] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:301:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] src/binarySequences.c:301:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] src/binarySequences.c:301:4: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat] src/binarySequences.c:301:4: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat] src/binarySequences.c:301:4: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat] src/binarySequences.c:311:12: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:386:2: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' [-Wformat] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:7: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat] src/preGraphConstruction.c:525:7: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wall -fopenmp -O3 -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o -lz -lm gcc -Wall -fopenmp -O3 -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o -lz -lm cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../.. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./Manual.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size10.clo)) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))) No file Manual.aux. (/usr/share/texmf-texlive/tex/latex/graphics/color.sty (/etc/texmf/tex/latex/config/color.cfg)) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, total 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, total 100165,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, total 100122,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [2] LaTeX Warning: Reference `sec:kmercov' on page 3 undefined on input line 115. [3] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [4] LaTeX Warning: Reference `sec:kmercov' on page 5 undefined on input line 192. Overfull \hbox (101.24611pt too wide) in paragraph at lines 222--222 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] [5] Overfull \hbox (17.24684pt too wide) in paragraph at lines 242--242 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 249--249 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 257--257 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [6] [7] LaTeX Warning: Reference `sec:covcutoff' on page 8 undefined on input line 332. Overfull \hbox (43.49661pt too wide) in paragraph at lines 342--342 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 8 undefined on input line 355. LaTeX Warning: Reference `sec:kmercov' on page 8 undefined on input line 359. LaTeX Warning: Reference `sec:expcov' on page 8 undefined on input line 359. Overfull \hbox (11.99689pt too wide) in paragraph at lines 363--363 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [8] Overfull \hbox (22.4968pt too wide) in paragraph at lines 369--369 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] LaTeX Warning: Reference `sec:hashing' on page 9 undefined on input line 378. LaTeX Warning: Reference `sec:kmercov' on page 9 undefined on input line 380. LaTeX Warning: Reference `sec:pairedformat' on page 9 undefined on input line 3 96. Overfull \hbox (22.4968pt too wide) in paragraph at lines 407--407 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [9] [10] Overfull \hbox (32.9967pt too wide) in paragraph at lines 452--452 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:amos' on page 11 undefined on input line 456. Overfull \hbox (32.9967pt too wide) in paragraph at lines 460--460 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 11 undefined on input line 471. Overfull \hbox (48.74657pt too wide) in paragraph at lines 490--490 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 498--499 []$[]$\OT1/cmr/m/n/10 . If set LaTeX Warning: Reference `sec:paper' on page 11 undefined on input line 500. [11] Overfull \hbox (59.24648pt too wide) in paragraph at lines 515--515 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 523--523 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 531--531 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [12] Overfull \hbox (38.24666pt too wide) in paragraph at lines 547--547 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 566--566 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] LaTeX Warning: Reference `sec:kmercov' on page 13 undefined on input line 584. [13] LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 596. Overfull \hbox (8.06886pt too wide) in paragraph at lines 596--597 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov LaTeX Warning: Reference `sec:fasta' on page 14 undefined on input line 606. (/usr/share/texmf-texlive/tex/latex/base/omscmr.fd) [14] Overfull \hbox (73.7466pt too wide) in paragraph at lines 629--629 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] LaTeX Warning: Reference `sec:stats' on page 15 undefined on input line 633. Overfull \hbox (36.99692pt too wide) in paragraph at lines 647--647 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [15] LaTeX Warning: Reference `sec:maxlength' on page 16 undefined on input line 674 . LaTeX Warning: Reference `sec:paper' on page 16 undefined on input line 686. LaTeX Warning: Reference `sec:kmercov' on page 16 undefined on input line 686. <./Suis_plot_1.pdf, id=127, 614.295pt x 505.89pt> [16] <./suis_plot.pdf, id=134, 614.295pt x 505.89pt> [17 <./Suis_plot_1.pdf>] [18 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 759--760 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [19] Overfull \hbox (47.5168pt too wide) in paragraph at lines 777--778 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [20] [21] (./Manual.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) Output written on Manual.pdf (21 pages, 468115 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./Manual.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size10.clo)) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))) (./Manual.aux) (/usr/share/texmf-texlive/tex/latex/graphics/color.sty (/etc/texmf/tex/latex/config/color.cfg)) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./Manual.out) (./Manual.out) (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (./Manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, total 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, total 100165,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, total 100122,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [3] [4] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [5] Overfull \hbox (101.24611pt too wide) in paragraph at lines 222--222 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] [6] Overfull \hbox (17.24684pt too wide) in paragraph at lines 242--242 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 249--249 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 257--257 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [7] [8] Overfull \hbox (43.49661pt too wide) in paragraph at lines 342--342 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 363--363 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [9] Overfull \hbox (22.4968pt too wide) in paragraph at lines 369--369 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 407--407 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [10] [11] Overfull \hbox (32.9967pt too wide) in paragraph at lines 452--452 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 460--460 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 490--490 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 498--499 []$[]$\OT1/cmr/m/n/10 . If set [12] Overfull \hbox (59.24648pt too wide) in paragraph at lines 515--515 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 523--523 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 531--531 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [13] Overfull \hbox (38.24666pt too wide) in paragraph at lines 547--547 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 566--566 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [14] Overfull \hbox (8.06886pt too wide) in paragraph at lines 596--597 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov (/usr/share/texmf-texlive/tex/latex/base/omscmr.fd) [15] Overfull \hbox (73.7466pt too wide) in paragraph at lines 629--629 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] Overfull \hbox (36.99692pt too wide) in paragraph at lines 647--647 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [16] <./Suis_plot_1.pdf, id=330, 614.295pt x 505.89pt> [17] <./suis_plot.pdf, id=335, 614.295pt x 505.89pt> [18 <./Suis_plot_1.pdf>] [19 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 759--760 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [20] Overfull \hbox (47.5168pt too wide) in paragraph at lines 777--778 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [21] [22] (./Manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Manual.pdf (22 pages, 493298 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./Columbus_manual.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size12.clo)) No file Columbus_manual.aux. Overfull \hbox (14.63878pt too wide) in paragraph at lines 36--37 []\OT1/cmr/m/n/12 You se-quenced an in-di-vid-ual genome by WGS, mapped [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/usr/share/texmf-texlive/tex/latex/base/omscmr.fd) [3] [4] Overfull \hbox (5.12076pt too wide) in paragraph at lines 132--134 []\OT1/cmr/m/n/12 This scripts adds an ar-bi-trary buffer length (de-fault $100 \OML/cmm/m/it/12 bp$\OT1/cmr/m/n/12 ) Overfull \hbox (36.07521pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 grep exon my_annotation.gtf | enlarge_exons.pl | merge_gtf_e xons.pl \[] Overfull \hbox (23.7252pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 | gff2fasta.pl my_reference_assembly.fa > my_reference_seque nces.fa[] [5] (./Columbus_manual.aux) ) (see the transcript file for additional information) Output written on Columbus_manual.pdf (5 pages, 95937 bytes). Transcript written on Columbus_manual.log. make[2]: Leaving directory `/«PKGBUILDDIR»' dh_auto_build -- color OPENMP=1 make[2]: Entering directory `/«PKGBUILDDIR»' rm obj/*.o obj/dbg/*.o rm: cannot remove `obj/dbg/*.o': No such file or directory make[2]: [cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run.c -o obj/run.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1060:14: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run2.c -o obj/run2.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedGraph.c -o obj/concatenatedGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/passageMarker.c -o obj/passageMarker.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o src/graphStats.c: In function 'collectReferenceCoords': src/graphStats.c:1961:3: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long int' [-Wformat] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/correctedGraph.c -o obj/correctedGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:245:3: warning: case label value is less than minimum value for type [enabled by default] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:301:69: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] src/binarySequences.c:301:111: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] src/binarySequences.c:301:4: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat] src/binarySequences.c:301:4: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat] src/binarySequences.c:301:4: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'long long unsigned int' [-Wformat] src/binarySequences.c:311:12: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] src/binarySequences.c: In function 'moveCnySeqNucleotides': src/binarySequences.c:386:2: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t' [-Wformat] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/shortReadPairs.c -o obj/shortReadPairs.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/roadMap.c -o obj/roadMap.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraph.c -o obj/preGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:525:7: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'long long unsigned int' [-Wformat] src/preGraphConstruction.c:525:7: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'long long unsigned int' [-Wformat] gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readCoherentGraph.c -o obj/readCoherentGraph.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmer.c -o obj/kmer.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/scaffold.c -o obj/scaffold.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o gcc -Wall -fopenmp -O3 -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o -lz -lm gcc -Wall -fopenmp -O3 -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o -lz -lm make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch --with quilt dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory `/«PKGBUILDDIR»' mkdir -p /«PKGBUILDDIR»/debian/velvet/usr/share/man/man1/ help2man --no-info --name="simple hashing program" \ /«PKGBUILDDIR»/velveth > /«PKGBUILDDIR»/debian/velvet/usr/share/man/man1/velveth.1 help2man --no-info --name="simple hashing program (colorspace version)" \ /«PKGBUILDDIR»/velveth_de > /«PKGBUILDDIR»/debian/velvet/usr/share/man/man1/velveth_de.1 help2man --no-info --version-option=" " \ --name="de Bruijn graph construction, error removal and repeat resolution" \ /«PKGBUILDDIR»/velvetg > /«PKGBUILDDIR»/debian/velvet/usr/share/man/man1/velvetg.1 help2man --no-info --version-option=" " \ --name="de Bruijn graph construction, error removal and repeat resolution (colorspace version)" \ /«PKGBUILDDIR»/velvetg_de > /«PKGBUILDDIR»/debian/velvet/usr/share/man/man1/velvetg_de.1 dh_install #If the tarball is not being scrubbed we need this. # find /«PKGBUILDDIR»/debian/velvet -name '.DS_Store' -exec rm {} \; rmdir /«PKGBUILDDIR»/debian/velvet/usr/share/velvet/contrib/MetaVelvet-v0.3.1/obj make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a debian/rules override_dh_compress make[1]: Entering directory `/«PKGBUILDDIR»' dh_compress -X.pdf make[1]: Leaving directory `/«PKGBUILDDIR»' dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package velvet: unused substitution variable ${perl:Depends} dh_md5sums -a debian/rules override_dh_builddeb make[1]: Entering directory `/«PKGBUILDDIR»' dh_builddeb -- -Z xz dpkg-deb: building package `velvet' in `../velvet_1.2.03~nozlibcopy-1_armhf.deb'. make[1]: Leaving directory `/«PKGBUILDDIR»' dpkg-genchanges -B -mbuildd >../velvet_1.2.03~nozlibcopy-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build velvet-1.2.03~nozlibcopy dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120504-2325 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ velvet_1.2.03~nozlibcopy-1_armhf.changes: ───────────────────────────────────────── Format: 1.8 Date: Thu, 16 Feb 2012 13:37:19 +0900 Source: velvet Binary: velvet velvet-example Architecture: armhf Version: 1.2.03~nozlibcopy-1 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Charles Plessy Description: velvet - Nucleic acid sequence assembler for very short reads velvet-example - Example data for the Velvet sequence assembler Changes: velvet (1.2.03~nozlibcopy-1) unstable; urgency=low . * New upstream release. * Updated debian/patches/include_debians_zlib.patch. Checksums-Sha1: ce9d3bfc737cb89e98a4709b9c6a86376f7bb5db 688852 velvet_1.2.03~nozlibcopy-1_armhf.deb Checksums-Sha256: 52c9bc31d70112758d33ccf5239fead8b0481b10fccca78c959baab7e55ebadd 688852 velvet_1.2.03~nozlibcopy-1_armhf.deb Files: 6bcbdd85eea6b65ee88c94940864fb00 688852 science optional velvet_1.2.03~nozlibcopy-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ velvet_1.2.03~nozlibcopy-1_armhf.deb ──────────────────────────────────── new debian package, version 2.0. size 688852 bytes: control archive= 4004 bytes. 957 bytes, 21 lines control 10070 bytes, 112 lines md5sums Package: velvet Version: 1.2.03~nozlibcopy-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 2192 Pre-Depends: dpkg (>= 1.15.6) Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.4), zlib1g (>= 1:1.2.6) Recommends: python Suggests: velvet-example Section: science Priority: optional Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Description: Nucleic acid sequence assembler for very short reads Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. drwxr-xr-x root/root 0 2012-05-04 23:24 ./ drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/ drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/share/ drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/share/velvet/ drwxr-xr-x root/root 0 2011-09-24 12:47 ./usr/share/velvet/contrib/ drwxr-xr-x root/root 0 2010-06-15 13:09 ./usr/share/velvet/contrib/columbus_scripts/ -rwxr-xr-x root/root 1254 2010-06-04 13:27 ./usr/share/velvet/contrib/columbus_scripts/merge_gtf_exons.pl -rwxr-xr-x root/root 392 2010-06-08 20:52 ./usr/share/velvet/contrib/columbus_scripts/enlarge_exons.pl -rwxr-xr-x root/root 877 2010-06-07 16:20 ./usr/share/velvet/contrib/columbus_scripts/gff2fasta.pl drwxr-xr-x root/root 0 2012-05-04 23:20 ./usr/share/velvet/contrib/select_paired/ -rwxr-xr-x root/root 2467 2012-05-04 23:20 ./usr/share/velvet/contrib/select_paired/select_paired.pl drwxr-xr-x root/root 0 2011-09-24 12:47 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./usr/share/velvet/shuffleSequences_fastq.pl drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/share/doc/velvet/ -rw-r--r-- root/root 4320 2012-01-30 16:21 ./usr/share/doc/velvet/changelog.gz -rw-r--r-- root/root 1117 2011-03-08 10:39 ./usr/share/doc/velvet/README.txt -rw-r--r-- root/root 3463 2012-02-15 20:37 ./usr/share/doc/velvet/changelog.Debian.gz -rw-r--r-- root/root 1956 2011-03-29 22:36 ./usr/share/doc/velvet/CREDITS.txt -rw-r--r-- root/root 4356 2012-02-15 20:35 ./usr/share/doc/velvet/copyright -rw-r--r-- root/root 183 2009-07-11 08:34 ./usr/share/doc/velvet/README.Debian -rw-r--r-- root/root 493298 2012-05-04 23:22 ./usr/share/doc/velvet/Manual.pdf drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/share/doc-base/ -rw-r--r-- root/root 243 2008-06-19 19:19 ./usr/share/doc-base/velvet drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/share/man/man1/ -rw-r--r-- root/root 1255 2012-05-04 23:24 ./usr/share/man/man1/velveth.1.gz -rw-r--r-- root/root 1711 2012-05-04 23:24 ./usr/share/man/man1/velvetg.1.gz -rw-r--r-- root/root 1729 2012-05-04 23:24 ./usr/share/man/man1/velvetg_de.1.gz -rw-r--r-- root/root 1274 2012-05-04 23:24 ./usr/share/man/man1/velveth_de.1.gz drwxr-xr-x root/root 0 2012-05-04 23:24 ./usr/bin/ -rwxr-xr-x root/root 294840 2012-05-04 23:24 ./usr/bin/velvetg -rwxr-xr-x root/root 294584 2012-05-04 23:24 ./usr/bin/velvetg_de -rwxr-xr-x root/root 75784 2012-05-04 23:24 ./usr/bin/velveth -rwxr-xr-x root/root 76984 2012-05-04 23:24 ./usr/bin/velveth_de ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* diffstat* ed* file* fontconfig-config* gettext* gettext-base* groff-base* help2man* html2text* intltool-debian* libcroco3* libexpat1* libffi5* libfontconfig1* libfreetype6* libglib2.0-0* libice6* libjpeg8* libkpathsea5* liblcms1* libmagic1* libopenjpeg2* libpaper-utils* libpaper1* libpcre3* libpipeline1* libpng12-0* libpoppler13* libsm6* libunistring0* libx11-6* libx11-data* libxau6* libxaw7* libxcb1* libxdmcp6* libxext6* libxml2* libxmu6* libxpm4* libxt6* luatex* man-db* mime-support* po-debconf* quilt* sbuild-build-depends-core-dummy* sbuild-build-depends-velvet-dummy* tex-common* texlive-base* texlive-binaries* texlive-common* texlive-doc-base* texlive-latex-base* ttf-dejavu-core* x11-common* zlib1g-dev* 0 upgraded, 0 newly installed, 59 to remove and 0 not upgraded. After this operation, 99.1 MB disk space will be freed. (Reading database ... 16312 files and directories currently installed.) Removing sbuild-build-depends-velvet-dummy ... Removing quilt ... Purging configuration files for quilt ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing diffstat ... Removing texlive-latex-base ... Purging configuration files for texlive-latex-base ... Removing texlive-base ... Purging configuration files for texlive-base ... Removing texlive-binaries ... Removing ed ... Removing file ... Removing luatex ... Removing libpoppler13 ... Purging configuration files for libpoppler13 ... Removing libfontconfig1:armhf ... Purging configuration files for libfontconfig1:armhf ... Removing fontconfig-config ... Purging configuration files for fontconfig-config ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing help2man ... 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Removing zlib1g-dev:armhf ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 45916 Build-Time: 306 Distribution: testing Install-Time: 170 Job: velvet_1.2.03~nozlibcopy-1 Package: velvet Package-Time: 499 Source-Version: 1.2.03~nozlibcopy-1 Space: 45916 Status: successful Version: 1.2.03~nozlibcopy-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120504-2325 Build needed 00:08:19, 45916k disc space