sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build02.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ cd-hit 4.6-2012-04-25-1 (armhf) 10 May 2012 15:05 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: cd-hit Version: 4.6-2012-04-25-1 Source Version: 4.6-2012-04-25-1 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/cd-hit-ZwV1wq/cd-hit-4.6-2012-04-25' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/cd-hit-ZwV1wq' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-d79248d4-bc5a-48a5-9b05-18bf813f828f' 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: 'cd-hit' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/cd-hit/trunk/ Need to get 659 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main cd-hit 4.6-2012-04-25-1 (dsc) [1427 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main cd-hit 4.6-2012-04-25-1 (tar) [652 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main cd-hit 4.6-2012-04-25-1 (diff) [5670 B] Fetched 659 kB in 0s (6953 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-0_D945/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 13 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 (>= 9), mpi-default-dev, help2man Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), mpi-default-dev, help2man dpkg-deb: building package `sbuild-build-depends-cd-hit-dummy' in `/«BUILDDIR»/resolver-eBYYVA/apt_archive/sbuild-build-depends-cd-hit-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install cd-hit build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: adduser bsdmainutils debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libffi5 libgfortran3 libglib2.0-0 libibverbs-dev libibverbs1 libmagic1 libopenmpi-dev libopenmpi1.3 libpcre3 libpipeline1 libtorque2 libunistring0 libxml2 man-db mpi-default-dev openmpi-common po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: adduser bsdmainutils debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libffi5 libgfortran3 libglib2.0-0 libibverbs-dev libibverbs1 libmagic1 libopenmpi-dev libopenmpi1.3 libpcre3 libpipeline1 libtorque2 libunistring0 libxml2 man-db mpi-default-dev openmpi-common po-debconf sbuild-build-depends-cd-hit-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 29 newly installed, 0 to remove and 13 not upgraded. Need to get 0 B/13.8 MB of archives. After this operation, 40.4 MB of additional disk space will be used. 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 libgfortran3:armhf. Unpacking libgfortran3:armhf (from .../libgfortran3_4.7.0-1.1+rpi_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package adduser. Unpacking adduser (from .../adduser_3.113+nmu1_all.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 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 help2man. Unpacking help2man (from .../help2man_1.40.9_armhf.deb) ... Selecting previously unselected package libtorque2. Unpacking libtorque2 (from .../libtorque2_2.4.16+dfsg-1_armhf.deb) ... Selecting previously unselected package libibverbs1. Unpacking libibverbs1 (from .../libibverbs1_1.1.6-1_armhf.deb) ... Selecting previously unselected package libibverbs-dev. Unpacking libibverbs-dev (from .../libibverbs-dev_1.1.6-1_armhf.deb) ... Selecting previously unselected package libopenmpi1.3. Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.4.3-2.1_armhf.deb) ... Selecting previously unselected package openmpi-common. Unpacking openmpi-common (from .../openmpi-common_1.4.3-2.1_all.deb) ... Selecting previously unselected package libopenmpi-dev. Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.4.3-2.1_armhf.deb) ... Selecting previously unselected package mpi-default-dev. Unpacking mpi-default-dev (from .../mpi-default-dev_1.0.1_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-cd-hit-dummy. Unpacking sbuild-build-depends-cd-hit-dummy (from .../sbuild-build-depends-cd-hit-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 libgfortran3:armhf (4.7.0-1.1+rpi) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up adduser (3.113+nmu1) ... 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 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 help2man (1.40.9) ... Setting up libtorque2 (2.4.16+dfsg-1) ... Setting up libibverbs1 (1.1.6-1) ... Setting up libibverbs-dev (1.1.6-1) ... Setting up libopenmpi1.3 (1.4.3-2.1) ... Setting up openmpi-common (1.4.3-2.1) ... Setting up libopenmpi-dev (1.4.3-2.1) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode. Setting up mpi-default-dev (1.0.1) ... Setting up sbuild-build-depends-cd-hit-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: adduser_3.113+nmu1 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 diffutils_1:3.2-2 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 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 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libgfortran3_4.7.0-1.1+rpi libglib2.0-0_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi libibverbs-dev_1.1.6-1 libibverbs1_1.1.6-1 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 libopenmpi-dev_1.4.3-2.1 libopenmpi1.3_1.4.3-2.1 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_1:8.30-4 libpipeline1_1.2.1-1 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 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 libtorque2_2.4.16+dfsg-1 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 libxml2_2.7.8.dfsg-9 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 mpi-default-dev_1.0.1 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-6 openmpi-common_1.4.3-2.1 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 readline-common_6.2-8 sbuild-build-depends-cd-hit-dummy_0.invalid.0 sbuild-build-depends-core-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 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Apr 26 09:18:55 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./cd-hit_4.6-2012-04-25-1.dsc dpkg-source: info: extracting cd-hit in cd-hit-4.6-2012-04-25 dpkg-source: info: unpacking cd-hit_4.6-2012-04-25.orig.tar.gz dpkg-source: info: unpacking cd-hit_4.6-2012-04-25-1.debian.tar.gz dpkg-source: info: applying use-dpkg-buildflags.patch dpkg-source: info: applying enable_help2man.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-d79248d4-bc5a-48a5-9b05-18bf813f828f SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package cd-hit dpkg-buildpackage: source version 4.6-2012-04-25-1 dpkg-source --before-build cd-hit-4.6-2012-04-25 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' rm -f *.o cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_build -- openmp=yes make[2]: Entering directory `/«PKGBUILDDIR»' g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-common.c++ -c cdhit-common.c++: In member function 'void SequenceDB::DoClustering(const Options&)': cdhit-common.c++:2990:66: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t {aka unsigned int}' [-Wformat] g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-utility.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-est.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-est.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-est g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-2d.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-2d g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-est-2d.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-est-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-est-2d g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-div.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-div.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-div g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-454.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-454.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-454 make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_install -- PREFIX=debian/cd-hit/usr/lib/cd-hit make[2]: Entering directory `/«PKGBUILDDIR»' for prog in cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454; do \ install -m 0755 $prog debian/cd-hit/usr/lib/cd-hit; \ done install -m 0755 *.pl debian/cd-hit/usr/lib/cd-hit; make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory `/«PKGBUILDDIR»' mkdir -p /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1/ help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='quickly group sequences' \ /«PKGBUILDDIR»/cd-hit | \ sed -e 's/^cd-\(hit \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='quickly group sequences in db1 or db2 format' \ /«PKGBUILDDIR»/cd-hit-2d | \ sed -e 's/^cd-\(hit-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit-2d.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='run CD-HIT algorithm on RNA/DNA sequences' \ /«PKGBUILDDIR»/cd-hit-est | \ sed -e 's/^cd-\(hit-est \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit-est.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format' \ /«PKGBUILDDIR»/cd-hit-est-2d | \ sed -e 's/^cd-\(hit-est-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit-est-2d.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs' \ /«PKGBUILDDIR»/cd-hit-2d-para.pl > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cd-hit-2d-para.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs' \ /«PKGBUILDDIR»/cd-hit-para.pl > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cd-hit-para.1 # psi-cd-hit.pl is throwing some errors which are fixed using sed help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities' \ /«PKGBUILDDIR»/psi-cd-hit.pl | \ sed -e '/^Name "main::.*" used only once:/d' \ > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//psi-cd-hit.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ /«PKGBUILDDIR»/psi-cd-hit-2d.pl > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d.1 # FIXME: what is the difference between psi-cd-hit-2d.pl and psi-cd-hit-2d-g1.pl ? help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ /«PKGBUILDDIR»/psi-cd-hit-2d-g1.pl > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d-g1.1 # No help output from # cd-hit-div.pl # clstr2tree.pl # clstr_merge.pl # clstr_merge_noorder.pl # clstr_reduce.pl # clstr_renumber.pl # clstr_rev.pl # clstr_sort_by.pl # clstr_sort_prot_by # make_multi_seq # psi-cd-hit-local.pl -> even throws several "used only once: possible typo" errors make[1]: Leaving directory `/«PKGBUILDDIR»' 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 --exclude=.pdf make[1]: Leaving directory `/«PKGBUILDDIR»' dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-est-2d contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-div contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-454 contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-2d contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-est contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `cd-hit' in `../cd-hit_4.6-2012-04-25-1_armhf.deb'. dpkg-genchanges -B -mbuildd >../cd-hit_4.6-2012-04-25-1_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 cd-hit-4.6-2012-04-25 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120510-1510 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ cd-hit_4.6-2012-04-25-1_armhf.changes: ────────────────────────────────────── Format: 1.8 Date: Thu, 26 Apr 2012 07:54:23 +0200 Source: cd-hit Binary: cd-hit Architecture: armhf Version: 4.6-2012-04-25-1 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: cd-hit - suite of programs designed to quickly group sequences Changes: cd-hit (4.6-2012-04-25-1) unstable; urgency=low . * New upstream version incorporating the previous patches as well as the LaTeX source of the documentation * debian/patches/use-dpkg-buildflags.patch: Make sure hardening flags will really propagate * debian/{control,rules}: Use mpi version of cd-hit * README.Debian: Tell users that we are using mpi and they should ask for an alternative if needed * debian/*.1, debian/manpages: Deleted in favour of autogenerated manpages using help2man; Remark: the manually edited pages were slightly better regarding "SEE ALSO" and "AUTHORS" sections but it is better to auto-generate the pages to stay with changes of future versions * debian/rules: Use help2man 2 create manpages whereever possible * debian/patches/enable_help2man.patch: Fix some minor issues to get less error output in man pages Checksums-Sha1: 3e50e2bc076bb3e3dceddaeea88c92c7e81bac3c 695758 cd-hit_4.6-2012-04-25-1_armhf.deb Checksums-Sha256: f3a6d4d02e4d81fe47b19e37428ef403065c95962d8af2ec0941e324fa6d5964 695758 cd-hit_4.6-2012-04-25-1_armhf.deb Files: 6fd7c99cdd19c1c68f560f742abd24d7 695758 science optional cd-hit_4.6-2012-04-25-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ cd-hit_4.6-2012-04-25-1_armhf.deb ───────────────────────────────── new debian package, version 2.0. size 695758 bytes: control archive= 2140 bytes. 930 bytes, 17 lines control 3461 bytes, 52 lines md5sums Package: cd-hit Version: 4.6-2012-04-25-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1203 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.4.0), perl, mpi-default-bin Section: science Priority: optional Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ Description: suite of programs designed to quickly group sequences cd-hit contains a number of programs designed to quickly group sequences. cd-hit groups proteins into clusters that meet a user-defined similarity threshold. cd-hit-est is similar to cd-hit, but designed to group nucleotide sequences (without introns). cd-hit-est-2d is similar to cd-hit-2d but designed to compare two nucleotide datasets. A number of other related programs are also in this package. Please see the cd-hit user manual, also part of this package, for further information. drwxr-xr-x root/root 0 2012-05-10 15:10 ./ drwxr-xr-x root/root 0 2012-05-10 15:10 ./usr/ drwxr-xr-x root/root 0 2012-05-10 15:09 ./usr/lib/ drwxr-xr-x root/root 0 2012-05-10 15:10 ./usr/lib/cd-hit/ -rwxr-xr-x root/root 112020 2012-05-10 15:10 ./usr/lib/cd-hit/cd-hit -rwxr-xr-x root/root 196 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_renumber.pl -rwxr-xr-x root/root 2028 2012-05-10 15:09 ./usr/lib/cd-hit/psi-cd-hit.pl -rwxr-xr-x root/root 1670 2012-05-10 15:09 ./usr/lib/cd-hit/make_multi_seq.pl -rwxr-xr-x root/root 1529 2012-05-10 15:09 ./usr/lib/cd-hit/psi-cd-hit-2d-g1.pl -rwxr-xr-x root/root 806 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_sort_by.pl -rwxr-xr-x root/root 1160 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_reps_faa_rev.pl -rwxr-xr-x root/root 952 2012-05-10 15:09 ./usr/lib/cd-hit/clstr2tree.pl -rwxr-xr-x root/root 112020 2012-05-10 15:10 ./usr/lib/cd-hit/cd-hit-est -rwxr-xr-x root/root 112020 2012-05-10 15:10 ./usr/lib/cd-hit/cd-hit-2d -rwxr-xr-x root/root 1620 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_rev.pl -rwxr-xr-x root/root 112016 2012-05-10 15:10 ./usr/lib/cd-hit/cd-hit-div -rwxr-xr-x root/root 12596 2012-05-10 15:09 ./usr/lib/cd-hit/cd-hit-2d-para.pl -rwxr-xr-x root/root 3199 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_merge.pl -rwxr-xr-x root/root 387 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_select.pl -rwxr-xr-x root/root 1103 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_sql_tbl_sort.pl -rwxr-xr-x root/root 4503 2012-05-10 15:09 ./usr/lib/cd-hit/clstr2xml.pl -rwxr-xr-x root/root 2335 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_quality_eval_by_link.pl -rwxr-xr-x root/root 877 2012-05-10 15:09 ./usr/lib/cd-hit/cd-hit-div.pl -rwxr-xr-x root/root 57101 2012-05-10 15:09 ./usr/lib/cd-hit/psi-cd-hit-local.pl -rwxr-xr-x root/root 725 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_size_stat.pl -rwxr-xr-x root/root 1209 2012-05-10 15:09 ./usr/lib/cd-hit/clstr2txt.pl -rwxr-xr-x root/root 3465 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_quality_eval.pl -rwxr-xr-x root/root 112104 2012-05-10 15:10 ./usr/lib/cd-hit/cd-hit-454 -rwxr-xr-x root/root 555 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_select_rep.pl -rwxr-xr-x root/root 2190 2012-05-10 15:09 ./usr/lib/cd-hit/plot_len1.pl -rwxr-xr-x root/root 11859 2012-05-10 15:09 ./usr/lib/cd-hit/cd-hit-para.pl -rwxr-xr-x root/root 112020 2012-05-10 15:10 ./usr/lib/cd-hit/cd-hit-est-2d -rwxr-xr-x root/root 554 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_rep.pl -rwxr-xr-x root/root 2328 2012-05-10 15:09 ./usr/lib/cd-hit/psi-cd-hit-2d.pl -rwxr-xr-x root/root 2162 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_merge_noorder.pl -rwxr-xr-x root/root 2928 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_sql_tbl.pl -rwxr-xr-x root/root 3668 2012-05-10 15:09 ./usr/lib/cd-hit/plot_2d.pl -rwxr-xr-x root/root 464 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_cut.pl -rwxr-xr-x root/root 1000 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_reduce.pl -rwxr-xr-x root/root 1291 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_sort_prot_by.pl -rwxr-xr-x root/root 779 2012-05-10 15:09 ./usr/lib/cd-hit/clstr_size_histogram.pl drwxr-xr-x root/root 0 2012-05-10 15:09 ./usr/share/ drwxr-xr-x root/root 0 2012-05-10 15:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-10 15:10 ./usr/share/doc/cd-hit/ -rw-r--r-- root/root 908 2012-04-25 16:06 ./usr/share/doc/cd-hit/changelog.gz -rw-r--r-- root/root 987 2012-04-26 02:03 ./usr/share/doc/cd-hit/changelog.Debian.gz -rw-r--r-- root/root 362533 2012-04-25 16:06 ./usr/share/doc/cd-hit/cdhit-user-guide.pdf -rw-r--r-- root/root 1982 2012-04-22 00:31 ./usr/share/doc/cd-hit/copyright -rw-r--r-- root/root 303 2012-04-25 23:50 ./usr/share/doc/cd-hit/README.Debian drwxr-xr-x root/root 0 2012-05-10 15:09 ./usr/share/doc-base/ -rw-r--r-- root/root 753 2011-12-22 00:06 ./usr/share/doc-base/cd-hit drwxr-xr-x root/root 0 2012-05-10 15:09 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-10 15:10 ./usr/share/man/man1/ -rw-r--r-- root/root 1815 2012-05-10 15:09 ./usr/share/man/man1/cdhit-est.1.gz -rw-r--r-- root/root 1595 2012-05-10 15:09 ./usr/share/man/man1/psi-cd-hit.1.gz -rw-r--r-- root/root 1919 2012-05-10 15:09 ./usr/share/man/man1/cdhit-est-2d.1.gz -rw-r--r-- root/root 1697 2012-05-10 15:10 ./usr/share/man/man1/psi-cd-hit-2d-g1.1.gz -rw-r--r-- root/root 1658 2012-05-10 15:09 ./usr/share/man/man1/cdhit.1.gz -rw-r--r-- root/root 1691 2012-05-10 15:09 ./usr/share/man/man1/psi-cd-hit-2d.1.gz -rw-r--r-- root/root 1112 2012-05-10 15:09 ./usr/share/man/man1/cd-hit-para.1.gz -rw-r--r-- root/root 1688 2012-05-10 15:09 ./usr/share/man/man1/cdhit-2d.1.gz -rw-r--r-- root/root 1148 2012-05-10 15:09 ./usr/share/man/man1/cd-hit-2d-para.1.gz drwxr-xr-x root/root 0 2012-05-10 15:10 ./usr/bin/ lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/clstr_sort_by -> ../lib/cd-hit/clstr_sort_by.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/cdhit-2d -> ../lib/cd-hit/cd-hit-2d lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/clstr_reduce -> ../lib/cd-hit/clstr_reduce.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/psi-cd-hit -> ../lib/cd-hit/psi-cd-hit.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/psi-cd-hit-local -> ../lib/cd-hit/psi-cd-hit-local.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/make_multi_seq -> ../lib/cd-hit/make_multi_seq.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/cd-hit-div -> ../lib/cd-hit/cd-hit-div.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/clstr_merge -> ../lib/cd-hit/clstr_merge.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/cd-hit-para -> ../lib/cd-hit/cd-hit-para.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/clstr_renumber -> ../lib/cd-hit/clstr_renumber.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/clstr_sort_prot_by -> ../lib/cd-hit/clstr_sort_prot_by.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/cd-hit-2d-para -> ../lib/cd-hit/cd-hit-2d-para.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/cdhit-est-2d -> ../lib/cd-hit/cd-hit-est-2d lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/clstr_merge_noorder -> ../lib/cd-hit/clstr_merge_noorder.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/psi-cd-hit-2d -> ../lib/cd-hit/psi-cd-hit-2d.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/clstr2tree -> ../lib/cd-hit/clstr2tree.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/cdhit -> ../lib/cd-hit/cd-hit lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/clstr_rev -> ../lib/cd-hit/clstr_rev.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/psi-cd-hit-2d-g1 -> ../lib/cd-hit/psi-cd-hit-2d-g1.pl lrwxrwxrwx root/root 0 2012-05-10 15:10 ./usr/bin/cdhit-est -> ../lib/cd-hit/cd-hit-est ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser* bsdmainutils* debhelper* file* gettext* gettext-base* groff-base* help2man* html2text* intltool-debian* libcroco3* libffi5* libgfortran3* libglib2.0-0* libibverbs-dev* libibverbs1* libmagic1* libopenmpi-dev* libopenmpi1.3* libpcre3* libpipeline1* libtorque2* libunistring0* libxml2* man-db* mpi-default-dev* openmpi-common* po-debconf* sbuild-build-depends-cd-hit-dummy* sbuild-build-depends-core-dummy* 0 upgraded, 0 newly installed, 30 to remove and 13 not upgraded. After this operation, 40.4 MB disk space will be freed. (Reading database ... 13042 files and directories currently installed.) Removing sbuild-build-depends-cd-hit-dummy ... Removing mpi-default-dev ... Removing libopenmpi-dev ... Removing libopenmpi1.3 ... Purging configuration files for libopenmpi1.3 ... Removing libibverbs-dev ... Removing libibverbs1 ... Purging configuration files for libibverbs1 ... Removing adduser ... Purging configuration files for adduser ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing file ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing help2man ... Removing html2text ... Purging configuration files for html2text ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libgfortran3:armhf ... Purging configuration files for libgfortran3:armhf ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libtorque2 ... Purging configuration files for libtorque2 ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing openmpi-common ... Removing sbuild-build-depends-core-dummy ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 10164 Build-Time: 228 Distribution: testing Install-Time: 84 Job: cd-hit_4.6-2012-04-25-1 Package: cd-hit Package-Time: 329 Source-Version: 4.6-2012-04-25-1 Space: 10164 Status: successful Version: 4.6-2012-04-25-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120510-1510 Build needed 00:05:29, 10164k disc space