rsem →
1.2.26+dfsg-1 →
armhf → 2016-02-07 12:28:41
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testbuildd.raspbian.org
+==============================================================================+
| rsem 1.2.26+dfsg-1 (armhf) 07 Feb 2016 12:18 |
+==============================================================================+
Package: rsem
Version: 1.2.26+dfsg-1
Source Version: 1.2.26+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/rsem-EUfXyG/rsem-1.2.26+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/rsem-EUfXyG' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-40310303-5791-457e-8567-d4bf48137317' with '<<CHROOT>>'
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| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8671 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.7 MB]
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| Fetch source files |
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Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'rsem' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/debian-med/rsem.git
Please use:
git clone https://anonscm.debian.org/debian-med/rsem.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 144 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main rsem 1.2.26+dfsg-1 (dsc) [2028 B]
Get:2 http://172.17.0.1/private stretch-staging/main rsem 1.2.26+dfsg-1 (tar) [135 kB]
Get:3 http://172.17.0.1/private stretch-staging/main rsem 1.2.26+dfsg-1 (diff) [6980 B]
Fetched 144 kB in 0s (854 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-QKg6iJ/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-QKg6iJ/apt_archive ./ InRelease
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Get:2 file:/<<BUILDDIR>>/resolver-QKg6iJ/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-QKg6iJ/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-QKg6iJ/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-QKg6iJ/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-QKg6iJ/apt_archive ./ Packages [527 B]
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+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
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Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
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Get:1 file:/<<BUILDDIR>>/resolver-QKg6iJ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
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Merged Build-Depends: debhelper (>= 9), zlib1g-dev, libncurses5-dev, libbam-dev, libboost-dev, perl, bowtie | bowtie2
Filtered Build-Depends: debhelper (>= 9), zlib1g-dev, libncurses5-dev, libbam-dev, libboost-dev, perl, bowtie
dpkg-deb: building package 'sbuild-build-depends-rsem-dummy' in '/<<BUILDDIR>>/resolver-P_NTGz/apt_archive/sbuild-build-depends-rsem-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-P_NTGz/apt_archive ./ InRelease
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Get:2 file:/<<BUILDDIR>>/resolver-P_NTGz/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-P_NTGz/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-P_NTGz/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-P_NTGz/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-P_NTGz/apt_archive ./ Sources [251 B]
Get:5 file:/<<BUILDDIR>>/resolver-P_NTGz/apt_archive ./ Packages [559 B]
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+------------------------------------------------------------------------------+
| Install rsem build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autotools-dev bowtie bsdmainutils debhelper dh-strip-nondeterminism file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbam-dev libboost-dev libboost1.58-dev libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libncurses5-dev libpipeline1 libtimedate-perl libtinfo-dev libunistring0
libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
bowtie-examples wamerican | wordlist whois vacation dh-make gettext-doc
autopoint libasprintf-dev libgettextpo-dev groff libboost-doc
libboost1.58-doc libboost-atomic1.58-dev libboost-chrono1.58-dev
libboost-context1.58-dev libboost-coroutine1.58-dev
libboost-date-time1.58-dev libboost-exception1.58-dev
libboost-filesystem1.58-dev libboost-graph1.58-dev
libboost-graph-parallel1.58-dev libboost-iostreams1.58-dev
libboost-locale1.58-dev libboost-log1.58-dev libboost-math1.58-dev
libboost-mpi1.58-dev libboost-mpi-python1.58-dev
libboost-program-options1.58-dev libboost-python1.58-dev
libboost-random1.58-dev libboost-regex1.58-dev
libboost-serialization1.58-dev libboost-signals1.58-dev
libboost-system1.58-dev libboost-test1.58-dev libboost-thread1.58-dev
libboost-timer1.58-dev libboost-wave1.58-dev libboost1.58-tools-dev
libmpfrc++-dev libntl-dev ncurses-doc less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autotools-dev bowtie bsdmainutils debhelper dh-strip-nondeterminism file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbam-dev libboost-dev libboost1.58-dev libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libncurses5-dev libpipeline1 libtimedate-perl libtinfo-dev libunistring0
libxml2 man-db po-debconf sbuild-build-depends-rsem-dummy zlib1g-dev
0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 24.6 MB/24.6 MB of archives.
After this operation, 168 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-P_NTGz/apt_archive ./ sbuild-build-depends-rsem-dummy 0.invalid.0 [796 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.015-1 [6810 B]
Get:23 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160115 [827 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libboost1.58-dev armhf 1.58.0+dfsg-4.1 [6234 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.58.0.1 [3472 B]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20151024-2 [65.8 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libncurses5-dev armhf 6.0+20151024-2 [154 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf bowtie armhf 1.0.0-5 [1320 kB]
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Processing triggers for libc-bin (2.21-7) ...
Setting up groff-base (1.22.3-7) ...
Setting up bsdmainutils (9.0.6) ...
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 libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
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Setting up dh-strip-nondeterminism (0.015-1) ...
Processing triggers for libc-bin (2.21-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7+rpi1 gcc-5_5.3.1-7+rpi1 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7+rpi1 libstdc++6_5.3.1-7+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.113+nmu3 apt_1.2.1 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-2 bowtie_1.0.0-5 bsdmainutils_9.0.6 bsdutils_1:2.27.1-3 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.24-1 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-7+rpi1 dash_0.5.8-2.1 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20160115 debianutils_4.7 dh-strip-nondeterminism_0.015-1 diffutils_1:3.3-3 dmsetup_2:1.02.115-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-7+rpi1 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-10 gcc-5_5.3.1-7+rpi1 gcc-5-base_5.3.1-7+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5.1 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-7+rpi1 kmod_22-1 libacl1_2.2.52-2 libapparmor1_2.10-3 libapt-pkg5.0_1.2.1 libarchive-zip-perl_1.56-2 libasan2_5.3.1-7+rpi1 libatomic1_5.3.1-7+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libbam-dev_0.1.19-2 libblkid1_2.27.1-3 libboost-dev_1.58.0.1 libboost1.58-dev_1.58.0+dfsg-4.1 libbz2-1.0_1.0.6-8 libc-bin_2.21-7 libc-dev-bin_2.21-7 libc6_2.21-7 libc6-dev_2.21-7 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-7+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.201 libdevmapper1.02.1_2:1.02.115-1 libdpkg-perl_1.18.4 libdrm2_2.4.66-2 libfakeroot_1.20.2-1 libfdisk1_2.27.1-3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.015-1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-7+rpi1 libgcc1_1:5.3.1-7+rpi1 libgcrypt20_1.6.4-5 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-7+rpi1 libgpg-error0_1.21-1 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-7+rpi1 libkmod2_22-1 liblz4-1_0.0~r131-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-3 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2 libncurses5-dev_6.0+20151024-2 libncursesw5_6.0+20151024-2 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-1 libperl5.22_5.22.1-5 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsmartcols1_2.27.1-3 libss2_1.42.13-1 libstdc++-5-dev_5.3.1-7+rpi1 libstdc++6_5.3.1-7+rpi1 libsystemd0_228-4+b1 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20151024-2 libtinfo5_6.0+20151024-2 libubsan0_5.3.1-7+rpi1 libudev1_228-4+b1 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-3 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 make_4.1-5 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-0.1 mawk_1.3.3-17 mount_2.27.1-3 multiarch-support_2.21-7 nano_2.5.1-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-5 perl-base_5.22.1-5 perl-modules-5.22_5.22.1-5 po-debconf_1.0.19 procps_2:3.3.11-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rsem-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_228-4+b1 systemd-sysv_228-4+b1 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2016a-1 udev_228-4+b1 util-linux_2.27.1-3 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Feb 1 07:27:46 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./rsem_1.2.26+dfsg-1.dsc
dpkg-source: info: extracting rsem in rsem-1.2.26+dfsg
dpkg-source: info: unpacking rsem_1.2.26+dfsg.orig.tar.gz
dpkg-source: info: unpacking rsem_1.2.26+dfsg-1.debian.tar.xz
dpkg-source: info: applying spelling
dpkg-source: info: applying ignore-sam
dpkg-source: info: applying fix-sam-includes
dpkg-source: info: applying fix-boost
dpkg-source: info: applying use-flags
dpkg-source: info: applying add-descriptions
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-40310303-5791-457e-8567-d4bf48137317
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package rsem
dpkg-buildpackage: source version 1.2.26+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build rsem-1.2.26+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
mkdir -p sam
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
rm -f *.o *~ rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
dh_clean -O--parallel
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
dh_auto_configure -a -O--parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
for prog in convert-sam-for-rsem rsem-calculate-expression \
rsem-control-fdr rsem-generate-ngvector \
rsem-plot-transcript-wiggles rsem-prepare-reference \
rsem-run-ebseq; do pod2man ${prog} debian/${prog}.1; done
dh_auto_build
make -j4
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
g++ -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
g++ -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -ffast-math -c -I. -I/usr/include preRef.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -c -I. parseIt.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -O3 buildReadIndex.cpp -o rsem-build-read-index
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -ffast-math -c -I. -I/usr/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security EM.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o rsem-tbam2gbam
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -ffast-math -c -I. -I/usr/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security Gibbs.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -ffast-math -c -I. -I/usr/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security calcCI.cpp
In file included from tbam2gbam.cpp:5:0:
utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
static bool verbose = true; // show detail intermediate outputs
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -ffast-math -c -I. -I/usr/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security simulation.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -ffast-math -c -I. -I/usr/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security wiggle.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o rsem-get-unique
In file included from wiggle.cpp:10:0:
utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
static bool verbose = true; // show detail intermediate outputs
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -O3 -Wall samValidator.cpp /usr/lib/libbam.a -lz -lpthread -o rsem-sam-validator
In file included from getUnique.cpp:12:0:
utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
static bool verbose = true; // show detail intermediate outputs
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o rsem-scan-for-paired-end-reads
In file included from samValidator.cpp:12:0:
utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
static bool verbose = true; // show detail intermediate outputs
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro preRef.o -o rsem-preref
g++ -Wl,-z,relro -o rsem-parse-alignments parseIt.o /usr/lib/libbam.a -lz -lpthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o rsem-run-gibbs Gibbs.o -lpthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o rsem-calculate-credibility-intervals calcCI.o -lpthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o rsem-bam2wig
In file included from scanForPairedEndReads.cpp:13:0:
utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
static bool verbose = true; // show detail intermediate outputs
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o rsem-bam2readdepth
g++ -Wl,-z,relro -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o rsem-simulate-reads simulation.o
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
dh_auto_test -a -O--parallel
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
find . -maxdepth 1 -type f -perm /u+x | xargs -n 1 -I{} dh_install {} /usr/bin/
dh_install rsem_perl_utils.pm /usr/share/perl5
dh_auto_install
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.26+dfsg'
dh_installdocs -a -O--parallel
dh_installchangelogs -a -O--parallel
dh_installman -a -O--parallel
dh_lintian -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
dh_fixperms -a -O--parallel
dh_strip -a -O--parallel
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-scan-for-paired-end-reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-build-read-index contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-run-gibbs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-parse-alignments contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-extract-reference-transcripts contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-bam2readdepth contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-run-em contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-preref contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-get-unique contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-calculate-credibility-intervals contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-tbam2gbam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-sam-validator contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-simulate-reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-synthesis-reference-transcripts contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-bam2wig contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/rsem/usr/bin/rsem-scan-for-paired-end-reads debian/rsem/usr/bin/rsem-build-read-index debian/rsem/usr/bin/rsem-run-gibbs debian/rsem/usr/bin/rsem-parse-alignments debian/rsem/usr/bin/rsem-extract-reference-transcripts debian/rsem/usr/bin/rsem-bam2readdepth debian/rsem/usr/bin/rsem-run-em debian/rsem/usr/bin/rsem-preref debian/rsem/usr/bin/rsem-get-unique debian/rsem/usr/bin/rsem-calculate-credibility-intervals debian/rsem/usr/bin/rsem-tbam2gbam debian/rsem/usr/bin/rsem-sam-validator debian/rsem/usr/bin/rsem-simulate-reads debian/rsem/usr/bin/rsem-synthesis-reference-transcripts debian/rsem/usr/bin/rsem-bam2wig were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.2.26+dfsg-1_armhf.deb'.
dpkg-deb: building package 'rsem' in '../rsem_1.2.26+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../rsem_1.2.26+dfsg-1_armhf.changes
dpkg-genchanges: warning: package rsem-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build rsem-1.2.26+dfsg
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160207-1227
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
rsem_1.2.26+dfsg-1_armhf.changes:
---------------------------------
Format: 1.8
Date: Sun, 31 Jan 2016 03:20:22 -0800
Source: rsem
Binary: rsem
Architecture: armhf
Version: 1.2.26+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <crusoe@ucdavis.edu>
Description:
rsem - RNA-Seq by Expectation-Maximization
Changes:
rsem (1.2.26+dfsg-1) unstable; urgency=medium
.
* New upstream release
Checksums-Sha1:
2965f2af2af6d8c0afed018bdacc535e2d22911b 3383668 rsem-dbgsym_1.2.26+dfsg-1_armhf.deb
76f54ef21eec5d7a550931d0f23f3ac4dc776947 399884 rsem_1.2.26+dfsg-1_armhf.deb
Checksums-Sha256:
684f3ba028a82743e139896f3a8194a07a507aed5962d07a72cf0523dc9f256e 3383668 rsem-dbgsym_1.2.26+dfsg-1_armhf.deb
4f46f33448f2c7781819090b0b69724e7276839cec5d8bbe7dc37db631178489 399884 rsem_1.2.26+dfsg-1_armhf.deb
Files:
8507ffcf95990cdad6ad6493be0a9378 3383668 debug extra rsem-dbgsym_1.2.26+dfsg-1_armhf.deb
c724524f412f8362bccaa2ee661fe33a 399884 science optional rsem_1.2.26+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
rsem-dbgsym_1.2.26+dfsg-1_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 3383668 bytes: control archive=1255 bytes.
991 bytes, 13 lines control
1590 bytes, 15 lines md5sums
Package: rsem-dbgsym
Source: rsem
Version: 1.2.26+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3840
Depends: rsem (= 1.2.26+dfsg-1)
Section: debug
Priority: extra
Homepage: http://deweylab.biostat.wisc.edu/rsem/
Description: Debug symbols for rsem
Auto-Built-Package: debug-symbols
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lrwxrwxrwx root/root 0 2016-02-07 12:26 ./usr/share/doc/rsem-dbgsym -> rsem
rsem_1.2.26+dfsg-1_armhf.deb
----------------------------
new debian package, version 2.0.
size 399884 bytes: control archive=2424 bytes.
1541 bytes, 27 lines control
2948 bytes, 43 lines md5sums
Package: rsem
Version: 1.2.26+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2274
Depends: libc6 (>= 2.15), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), perl, r-base-core, bowtie | bowtie2, python
Suggests: r-bioc-ebseq
Section: science
Priority: optional
Homepage: http://deweylab.biostat.wisc.edu/rsem/
Description: RNA-Seq by Expectation-Maximization
RSEM is a software package for estimating gene and isoform expression
levels from RNA-Seq data. The RSEM package provides an user-friendly
interface, supports threads for parallel computation of the EM
algorithm, single-end and paired-end read data, quality scores,
variable-length reads and RSPD estimation. In addition, it provides
posterior mean and 95% credibility interval estimates for expression
levels. For visualization, It can generate BAM and Wiggle files in both
transcript-coordinate and genomic-coordinate. Genomic-coordinate files
can be visualized by both UCSC Genome browser and Broad Institute’s
Integrative Genomics Viewer (IGV). Transcript-coordinate files can be
visualized by IGV. RSEM also has its own scripts to generate transcript
read depth plots in pdf format. The unique feature of RSEM is, the read
depth plots can be stacked, with read depth contributed to unique reads
shown in black and contributed to multi-reads shown in red. In addition,
models learned from data can also be visualized. Last but not least,
RSEM contains a simulator.
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drwxr-xr-x root/root 0 2016-02-07 12:26 ./usr/bin/
-rwxr-xr-x root/root 4307 2016-02-07 12:22 ./usr/bin/convert-sam-for-rsem
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-rwxr-xr-x root/root 105552 2016-02-07 12:26 ./usr/bin/rsem-bam2readdepth
-rwxr-xr-x root/root 105524 2016-02-07 12:26 ./usr/bin/rsem-bam2wig
-rwxr-xr-x root/root 14012 2016-02-07 12:26 ./usr/bin/rsem-build-read-index
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-rwxr-xr-x root/root 51669 2016-02-07 12:22 ./usr/bin/rsem-calculate-expression
-rwxr-xr-x root/root 3315 2016-02-07 12:22 ./usr/bin/rsem-control-fdr
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-rwxr-xr-x root/root 1979 2016-01-13 23:35 ./usr/bin/rsem-generate-data-matrix
-rwxr-xr-x root/root 3468 2016-02-07 12:22 ./usr/bin/rsem-generate-ngvector
-rwxr-xr-x root/root 101380 2016-02-07 12:26 ./usr/bin/rsem-get-unique
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-rwxr-xr-x root/root 15777 2016-02-07 12:22 ./usr/bin/rsem-prepare-reference
-rwxr-xr-x root/root 34572 2016-02-07 12:26 ./usr/bin/rsem-preref
-rwxr-xr-x root/root 495 2016-01-13 23:35 ./usr/bin/rsem-refseq-extract-primary-assembly
-rwxr-xr-x root/root 6430 2016-02-07 12:22 ./usr/bin/rsem-run-ebseq
-rwxr-xr-x root/root 392652 2016-02-07 12:26 ./usr/bin/rsem-run-em
-rwxr-xr-x root/root 219216 2016-02-07 12:26 ./usr/bin/rsem-run-gibbs
-rwxr-xr-x root/root 105512 2016-02-07 12:26 ./usr/bin/rsem-sam-validator
-rwxr-xr-x root/root 109584 2016-02-07 12:26 ./usr/bin/rsem-scan-for-paired-end-reads
-rwxr-xr-x root/root 215072 2016-02-07 12:26 ./usr/bin/rsem-simulate-reads
-rwxr-xr-x root/root 67384 2016-02-07 12:26 ./usr/bin/rsem-synthesis-reference-transcripts
-rwxr-xr-x root/root 162996 2016-02-07 12:26 ./usr/bin/rsem-tbam2gbam
drwxr-xr-x root/root 0 2016-02-07 12:26 ./usr/share/
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-rw-r--r-- root/root 9199 2016-02-07 12:22 ./usr/share/doc/rsem/README.md.gz
-rw-r--r-- root/root 4663 2016-01-13 23:35 ./usr/share/doc/rsem/WHAT_IS_NEW.gz
-rw-r--r-- root/root 329 2016-02-01 07:23 ./usr/share/doc/rsem/changelog.Debian.gz
-rw-r--r-- root/root 1398 2016-01-13 23:35 ./usr/share/doc/rsem/cnt_file_description.txt
-rw-r--r-- root/root 1089 2016-02-01 07:23 ./usr/share/doc/rsem/copyright
-rw-r--r-- root/root 1544 2016-01-13 23:35 ./usr/share/doc/rsem/model_file_description.txt.gz
drwxr-xr-x root/root 0 2016-02-07 12:26 ./usr/share/lintian/
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-rw-r--r-- root/root 300 2016-02-01 07:23 ./usr/share/lintian/overrides/rsem
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-rw-r--r-- root/root 3395 2016-01-13 23:35 ./usr/share/perl5/rsem_perl_utils.pm
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 36600
Build-Time: 286
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 216
Job: rsem_1.2.26+dfsg-1
Machine Architecture: armhf
Package: rsem
Package-Time: 548
Source-Version: 1.2.26+dfsg-1
Space: 36600
Status: successful
Version: 1.2.26+dfsg-1
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Finished at 20160207-1227
Build needed 00:09:08, 36600k disc space