rsem →
1.2.30+dfsg-1 →
armhf → 2016-05-21 12:53:59
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard
+==============================================================================+
| rsem 1.2.30+dfsg-1 (armhf) 21 May 2016 12:37 |
+==============================================================================+
Package: rsem
Version: 1.2.30+dfsg-1
Source Version: 1.2.30+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/rsem-_9ohYU/rsem-1.2.30+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/rsem-_9ohYU' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-5860eb1a-c215-443d-a5c4-026c23970ca3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8979 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
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+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
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Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'rsem' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/rsem.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/rsem.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4889 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main rsem 1.2.30+dfsg-1 (dsc) [2026 B]
Get:2 http://172.17.0.1/private stretch-staging/main rsem 1.2.30+dfsg-1 (tar) [4882 kB]
Get:3 http://172.17.0.1/private stretch-staging/main rsem 1.2.30+dfsg-1 (diff) [5012 B]
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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-5FZJIy/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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Get:3 file:/<<BUILDDIR>>/resolver-5FZJIy/apt_archive ./ Release.gpg [299 B]
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+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
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Building dependency tree...
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
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Merged Build-Depends: debhelper (>= 9), zlib1g-dev, libncurses5-dev, libboost-dev, perl, python, help2man, bowtie | bowtie2
Filtered Build-Depends: debhelper (>= 9), zlib1g-dev, libncurses5-dev, libboost-dev, perl, python, help2man, bowtie
dpkg-deb: building package 'sbuild-build-depends-rsem-dummy' in '/<<BUILDDIR>>/resolver-ABnzAx/apt_archive/sbuild-build-depends-rsem-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-ABnzAx/apt_archive ./ InRelease
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Get:3 file:/<<BUILDDIR>>/resolver-ABnzAx/apt_archive ./ Release.gpg [299 B]
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Get:4 file:/<<BUILDDIR>>/resolver-ABnzAx/apt_archive ./ Sources [237 B]
Get:5 file:/<<BUILDDIR>>/resolver-ABnzAx/apt_archive ./ Packages [547 B]
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W: file:///<<BUILDDIR>>/resolver-ABnzAx/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| 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:
autoconf automake autopoint autotools-dev bowtie bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libboost-dev libboost1.58-dev
libbsd0 libcroco3 libexpat1 libffi6 libfile-stripnondeterminism-perl
libglib2.0-0 libicu55 libmagic1 libncurses5-dev libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libsqlite3-0 libssl1.0.2 libtimedate-perl libtinfo-dev libtool libunistring0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc bowtie-examples wamerican
| wordlist whois vacation dh-make gettext-doc 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 libtool-doc gfortran
| fortran95-compiler gcj-jdk less www-browser libmail-box-perl python-doc
python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bowtie bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libboost-dev libboost1.58-dev
libbsd0 libcroco3 libexpat1 libffi6 libfile-stripnondeterminism-perl
libglib2.0-0 libicu55 libmagic1 libncurses5-dev libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libsqlite3-0 libssl1.0.2 libtimedate-perl libtinfo-dev libtool libunistring0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal sbuild-build-depends-rsem-dummy zlib1g-dev
0 upgraded, 49 newly installed, 0 to remove and 3 not upgraded.
Need to get 23.8 MB/32.0 MB of archives.
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Get:1 file:/<<BUILDDIR>>/resolver-ABnzAx/apt_archive ./ sbuild-build-depends-rsem-dummy 0.invalid.0 [802 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 libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-9 [382 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-9 [1163 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
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Get:15 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-9 [271 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-1 [19.5 kB]
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Get:18 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
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Get:20 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
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Get:24 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
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Get:26 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-1 [2548 kB]
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Get:31 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
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Get:34 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libboost1.58-dev armhf 1.58.0+dfsg-5+b1 [6232 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.58.0.1+b1 [3748 B]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20160319-1 [65.7 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libncurses5-dev armhf 6.0+20160319-1 [153 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf bowtie armhf 1.0.0-5 [1320 kB]
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Unpacking libboost-dev:armhf (1.58.0.1+b1) ...
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Unpacking libtinfo-dev:armhf (6.0+20160319-1) ...
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Unpacking libncurses5-dev:armhf (6.0+20160319-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
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Unpacking bowtie (1.0.0-5) ...
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Preparing to unpack .../sbuild-build-depends-rsem-dummy.deb ...
Unpacking sbuild-build-depends-rsem-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-7) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up bsdmainutils (9.0.10) ...
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) ...
Not building database; man-db/auto-update is not 'true'.
Setting up mime-support (3.60) ...
Setting up libexpat1:armhf (2.1.1-1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libsqlite3-0:armhf (3.12.2-1) ...
Setting up libssl1.0.2:armhf (1.0.2h-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.11-9) ...
Setting up python2.7 (2.7.11-9) ...
Setting up libpython-stdlib:armhf (2.7.11-1) ...
Setting up python (2.7.11-1) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20160430.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2) ...
Setting up libglib2.0-0:armhf (2.48.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libtool (2.4.6-0.1) ...
Setting up help2man (1.47.4) ...
Setting up libboost1.58-dev:armhf (1.58.0+dfsg-5+b1) ...
Setting up libboost-dev:armhf (1.58.0.1+b1) ...
Setting up libtinfo-dev:armhf (6.0+20160319-1) ...
Setting up libncurses5-dev:armhf (6.0+20160319-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up bowtie (1.0.0-5) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-rsem-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.7 g++-5_5.3.1-19 gcc-5_5.3.1-19 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-19 libstdc++6_6.1.1-1+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.12 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-8 bowtie_1.0.0-5 bsdmainutils_9.0.10 bsdutils_1:2.28-5 build-essential_11.7 bzip2_1.0.6-8 console-setup_1.142 console-setup-linux_1.142 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-19 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.124-1 dpkg_1.18.7 dpkg-dev_1.18.7 e2fslibs_1.43~WIP.2016.03.15-2 e2fsprogs_1.43~WIP.2016.03.15-2 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-19 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_4.9.3-14 gcc-5_5.3.1-19 gcc-5-base_5.3.1-19 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-5 help2man_1.47.4 hostname_3.17 ifupdown_0.8.11 init_1.33 init-system-helpers_1.33 initscripts_2.88dsf-59.4 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 iproute2_4.3.0-1 kbd_2.0.3-2 keyboard-configuration_1.142 klibc-utils_2.0.4-8+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10-4 libapt-pkg5.0_1.2.12 libarchive-zip-perl_1.57-1 libasan2_5.3.1-19 libatm1_1:2.5.1-1.5 libatomic1_6.1.1-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.5.2-1+rpi1 libaudit1_1:2.5.2-1+rpi1 libblkid1_2.28-5 libboost-dev_1.58.0.1+b1 libboost1.58-dev_1.58.0+dfsg-5+b1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-7 libc-dev-bin_2.22-7 libc6_2.22-7 libc6-dev_2.22-7 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_6.1.1-1+rpi1 libcomerr2_1.43~WIP.2016.03.15-2 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.210 libdevmapper1.02.1_2:1.02.124-1 libdpkg-perl_1.18.7 libdrm2_2.4.68-1 libexpat1_2.1.1-1 libfakeroot_1.20.2-1 libfdisk1_2.28-5 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.4 libgcc-5-dev_5.3.1-19 libgcc1_1:6.1.1-1+rpi1 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.1-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_6.1.1-1+rpi1 libgpg-error0_1.22-2 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1.1 liblocale-gettext-perl_1.07-1+b1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.28-5 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160319-1 libncurses5-dev_6.0+20160319-1 libncursesw5_6.0+20160319-1 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_2:8.38-3.1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps5_2:3.3.11-3 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-9 libpython2.7-stdlib_2.7.11-9 libreadline6_6.3-8+b3 libseccomp2_2.3.0-1 libselinux1_2.5-2 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-5 libsqlite3-0_3.12.2-1 libss2_1.43~WIP.2016.03.15-2 libssl1.0.2_1.0.2h-1 libstdc++-5-dev_5.3.1-19 libstdc++6_6.1.1-1+rpi1 libsystemd0_229-5 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+20160319-1 libtinfo5_6.0+20160319-1 libtool_2.4.6-0.1 libubsan0_6.1.1-1+rpi1 libudev1_229-5 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5 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 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.06-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-5 multiarch-support_2.22-7 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 po-debconf_1.0.19 procps_2:3.3.11-3 psmisc_22.21-2.1 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-9 python2.7-minimal_2.7.11-9 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_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-5 systemd-sysv_229-5 sysv-rc_2.88dsf-59.4 sysvinit-utils_2.88dsf-59.4 tar_1.28-2.2+rpi1 tzdata_2016d-2 udev_229-5 util-linux_2.28-5 xkb-data_2.17-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun May 15 10:54:12 2016 UTC using RSA key ID 6C67E6E2
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./rsem_1.2.30+dfsg-1.dsc
dpkg-source: info: extracting rsem in rsem-1.2.30+dfsg
dpkg-source: info: unpacking rsem_1.2.30+dfsg.orig.tar.gz
dpkg-source: info: unpacking rsem_1.2.30+dfsg-1.debian.tar.xz
dpkg-source: info: applying hardening
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-5860eb1a-c215-443d-a5c4-026c23970ca3
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package rsem
dpkg-buildpackage: info: source version 1.2.30+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build rsem-1.2.30+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg'
rm -f *.o *~ rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads rsem-run-gibbs rsem-calculate-credibility-intervals
cd samtools-1.3 && make clean-all
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd htslib-1.3 && make clean
make[3]: Entering directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3/htslib-1.3'
cd test/dat && rm -f test_input_*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam*
rm -f test/*.tmp test/*.tmp.*
rm -f libhts.so libhts.so.*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
rm -f libhts.a bgzip htsfile tabix test/fieldarith test/hfile test/sam test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep
make[3]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3/htslib-1.3'
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3'
cd EBSeq && make clean
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/EBSeq'
rm -rf EBSeq rsem-for-ebseq-calculate-clustering-info blockmodeling gplots gtools gdata caTools bitops KernSmooth BiocInstaller *~
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/EBSeq'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+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-1.2.30+dfsg'
dh_auto_build -- BOOST=/usr/include prefix=debian/tmp
make -j4 BOOST=/usr/include prefix=debian/tmp
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg'
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp
cd samtools-1.3 && ./configure --without-curses && make -f Makefile samtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking location of HTSlib source tree... htslib-1.3
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
=== configuring in htslib-1.3 (/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3/htslib-1.3)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--without-curses' 'CFLAGS=-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security' 'LDFLAGS=-fPIE -pie -Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' --cache-file=/dev/null --srcdir=.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp
yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
make[3]: Entering directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3'
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.3"' > version.h
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Isamtools-1.3/htslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
bam_tview_curses.c:341:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
#warning "No curses library is available; tview with curses is disabled."
^
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
cd htslib-1.3 && make lib-static
make[4]: Entering directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3/htslib-1.3'
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.3"' > version.h
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/vlen.o cram/vlen.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/zfio.o cram/zfio.c
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
make[4]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3/htslib-1.3'
gcc -pthread -rdynamic -fPIE -pie -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a htslib-1.3/libhts.a -lm -lz -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg/samtools-1.3'
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o samtools-1.3/htslib-1.3/libhts.a -lz
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o samtools-1.3/htslib-1.3/libhts.a -lz
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o samtools-1.3/htslib-1.3/libhts.a -lz
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o samtools-1.3/htslib-1.3/libhts.a -lz
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o samtools-1.3/htslib-1.3/libhts.a -lz
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o samtools-1.3/htslib-1.3/libhts.a -lz
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o samtools-1.3/htslib-1.3/libhts.a -lz
g++ -fPIE -pie -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o samtools-1.3/htslib-1.3/libhts.a -lz
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+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
help2man ./rsem-gff3-to-gtf --no-info --version-string="1.2.30+dfsg" \
--name 'Convert GFF3 files to GTF files.' > \
debian/rsem-gff3-to-gtf.1
help2man ./rsem-bam2wig --no-info --version-string="1.2.30+dfsg" \
--name 'Convert BAM files to wiggle files.' > \
debian/rsem-bam2wig.1
help2man ./rsem-simulate-reads --no-info --version-string="1.2.30+dfsg" \
--name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \
debian/rsem-simulate-reads.1
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+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-1.2.30+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 -- BOOST=/usr/include prefix=debian/tmp
make -j4 install DESTDIR=/<<BUILDDIR>>/rsem-1.2.30\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no BOOST=/usr/include prefix=debian/tmp
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg'
install -d /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/samtools-1.3
install -p rsem-extract-reference-transcripts /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-extract-reference-transcripts ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-extract-reference-transcripts ; install -p rsem-synthesis-reference-transcripts /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-synthesis-reference-transcripts ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-synthesis-reference-transcripts ; install -p rsem-preref /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-preref ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-preref ; install -p rsem-build-read-index /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-build-read-index ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-build-read-index ; install -p rsem-simulate-reads /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-simulate-reads ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-simulate-reads ; install -p rsem-parse-alignments /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-parse-alignments ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-parse-alignments ; install -p rsem-run-em /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-run-em ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-run-em ; install -p rsem-tbam2gbam /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-tbam2gbam ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-tbam2gbam ; install -p rsem-bam2wig /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-bam2wig ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-bam2wig ; install -p rsem-bam2readdepth /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-bam2readdepth ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-bam2readdepth ; install -p rsem-get-unique /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-get-unique ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-get-unique ; install -p rsem-sam-validator /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-sam-validator ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-sam-validator ; install -p rsem-scan-for-paired-end-reads /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-scan-for-paired-end-reads ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-scan-for-paired-end-reads ; install -p rsem-run-gibbs /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-run-gibbs ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-run-gibbs ; install -p rsem-calculate-credibility-intervals /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-calculate-credibility-intervals ; strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-calculate-credibility-intervals ;
install -p samtools-1.3/samtools /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/samtools-1.3/samtools
strip /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/samtools-1.3/samtools
install -p rsem-prepare-reference /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-prepare-reference ; install -p rsem-calculate-expression /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-calculate-expression ; install -p rsem-refseq-extract-primary-assembly /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-refseq-extract-primary-assembly ; install -p rsem-gff3-to-gtf /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-gff3-to-gtf ; install -p rsem-plot-model /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-plot-model ; install -p rsem-plot-transcript-wiggles /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-plot-transcript-wiggles ; install -p rsem-gen-transcript-plots /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-gen-transcript-plots ; install -p rsem-generate-data-matrix /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem-generate-data-matrix ; install -p extract-transcript-to-gene-map-from-trinity /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/extract-transcript-to-gene-map-from-trinity ; install -p convert-sam-for-rsem /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/convert-sam-for-rsem ;
install -p -m 644 rsem_perl_utils.pm /<<BUILDDIR>>/rsem-1.2.30+dfsg/debian/rsemdebian/tmp/bin/rsem_perl_utils.pm
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.2.30+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
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_1.2.30+dfsg-1_armhf.deb'.
dpkg-deb: building package 'rsem' in '../rsem_1.2.30+dfsg-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../rsem_1.2.30+dfsg-1_armhf.changes
dpkg-genchanges: warning: package rsem-dbgsym listed in files list but not in control info
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build rsem-1.2.30+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160521-1253
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
rsem_1.2.30+dfsg-1_armhf.changes:
---------------------------------
Format: 1.8
Date: Sun, 15 May 2016 03:49:04 -0700
Source: rsem
Binary: rsem
Architecture: armhf
Version: 1.2.30+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
rsem - RNA-Seq by Expectation-Maximization
Changes:
rsem (1.2.30+dfsg-1) unstable; urgency=medium
.
* New upstream release
* Use upstream's modified samtools-1.3 as that is required for correct
operation
* re-enable hardening to match source changes
* generate manual pages for rsem-bam2wig & rsem-simulate-reads
Checksums-Sha1:
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2ee9ba1f2a0dbf02fc85c76fc15d753010000c9c 612592 rsem_1.2.30+dfsg-1_armhf.deb
Checksums-Sha256:
6965639874179d452348e597017c4b011e441c4d4ffd3955ad39945ab7c90d6f 7513770 rsem-dbgsym_1.2.30+dfsg-1_armhf.deb
b69f5484d2f671a9d3aa7d25e26bc696668970265c291c1ab90509cc5d0ef4f0 612592 rsem_1.2.30+dfsg-1_armhf.deb
Files:
7f8b054ef306e9f5371eecf6c2aec401 7513770 debug extra rsem-dbgsym_1.2.30+dfsg-1_armhf.deb
ce91a40d40d2d04885139ec78b1a2848 612592 science extra rsem_1.2.30+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
rsem-dbgsym_1.2.30+dfsg-1_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 7513770 bytes: control archive=1258 bytes.
991 bytes, 13 lines control
1590 bytes, 15 lines md5sums
Package: rsem-dbgsym
Source: rsem
Version: 1.2.30+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8046
Depends: rsem (= 1.2.30+dfsg-1)
Section: debug
Priority: extra
Homepage: http://deweylab.biostat.wisc.edu/rsem/
Description: Debug symbols for rsem
Auto-Built-Package: debug-symbols
Build-Ids: 25f2b98b87cec779691900de64588789cfcb7600 3d5ce4d08df288936beca7aae2fbabdc42bf74be 5393d4a714a059413112bf471e744eaecbc5f0f0 72d0e2d10106490eb10fcd894c67dc111508cd81 7c0b7c683f55b44913d20c514b4156b268905009 7d5526c8f2c8d9ea4a17e88a484bd01d87b9be18 99ac9c159620f9ceb063cb6d19f7721b126d682e 9cdf62453816f275c42d9f89b853f9c2b2faa6a2 a44ff0880b907b1263952befa2424eef780dcff9 b779ce1f9005cdfde643fe2ec006e3ad3813a2a9 bfc3947b82009ac1624eec4b07edb13e73d38ced c04497b71e4526ec3233d5bcf7e62f65edc923f8 d6926bd5f91006a53da2c05b6e8224b8144e89f1 f6f893ca95080736754f086131af79200050d9f4 fa6a595da105bfe051026753b2a1a2fe8edf2bcd
drwxr-xr-x root/root 0 2016-05-21 12:53 ./
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/25/
-rw-r--r-- root/root 1232308 2016-05-21 12:52 ./usr/lib/debug/.build-id/25/f2b98b87cec779691900de64588789cfcb7600.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/3d/
-rw-r--r-- root/root 606904 2016-05-21 12:52 ./usr/lib/debug/.build-id/3d/5ce4d08df288936beca7aae2fbabdc42bf74be.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/53/
-rw-r--r-- root/root 120156 2016-05-21 12:52 ./usr/lib/debug/.build-id/53/93d4a714a059413112bf471e744eaecbc5f0f0.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/72/
-rw-r--r-- root/root 796128 2016-05-21 12:52 ./usr/lib/debug/.build-id/72/d0e2d10106490eb10fcd894c67dc111508cd81.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/7c/
-rw-r--r-- root/root 617348 2016-05-21 12:52 ./usr/lib/debug/.build-id/7c/0b7c683f55b44913d20c514b4156b268905009.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/7d/
-rw-r--r-- root/root 561556 2016-05-21 12:52 ./usr/lib/debug/.build-id/7d/5526c8f2c8d9ea4a17e88a484bd01d87b9be18.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/99/
-rw-r--r-- root/root 290016 2016-05-21 12:52 ./usr/lib/debug/.build-id/99/ac9c159620f9ceb063cb6d19f7721b126d682e.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 702168 2016-05-21 12:52 ./usr/lib/debug/.build-id/9c/df62453816f275c42d9f89b853f9c2b2faa6a2.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/a4/
-rw-r--r-- root/root 624808 2016-05-21 12:52 ./usr/lib/debug/.build-id/a4/4ff0880b907b1263952befa2424eef780dcff9.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/b7/
-rw-r--r-- root/root 255540 2016-05-21 12:52 ./usr/lib/debug/.build-id/b7/79ce1f9005cdfde643fe2ec006e3ad3813a2a9.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 42684 2016-05-21 12:52 ./usr/lib/debug/.build-id/bf/c3947b82009ac1624eec4b07edb13e73d38ced.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/c0/
-rw-r--r-- root/root 624916 2016-05-21 12:52 ./usr/lib/debug/.build-id/c0/4497b71e4526ec3233d5bcf7e62f65edc923f8.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/d6/
-rw-r--r-- root/root 540124 2016-05-21 12:52 ./usr/lib/debug/.build-id/d6/926bd5f91006a53da2c05b6e8224b8144e89f1.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/f6/
-rw-r--r-- root/root 629740 2016-05-21 12:52 ./usr/lib/debug/.build-id/f6/f893ca95080736754f086131af79200050d9f4.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/lib/debug/.build-id/fa/
-rw-r--r-- root/root 562464 2016-05-21 12:52 ./usr/lib/debug/.build-id/fa/6a595da105bfe051026753b2a1a2fe8edf2bcd.debug
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-05-21 12:52 ./usr/share/doc/rsem-dbgsym -> rsem
rsem_1.2.30+dfsg-1_armhf.deb
----------------------------
new debian package, version 2.0.
size 612592 bytes: control archive=2499 bytes.
1538 bytes, 27 lines control
3172 bytes, 46 lines md5sums
Package: rsem
Version: 1.2.30+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4684
Depends: libc6 (>= 2.15), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.0.2), perl, r-base-core, bowtie | bowtie2, python
Suggests: r-bioc-ebseq
Section: science
Priority: extra
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.
drwxr-xr-x root/root 0 2016-05-21 12:52 ./
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/bin/
-rwxr-xr-x root/root 2917 2016-04-20 21:59 ./usr/bin/convert-sam-for-rsem
-rwxr-xr-x root/root 791 2016-04-20 21:59 ./usr/bin/extract-transcript-to-gene-map-from-trinity
-rwxr-xr-x root/root 403004 2016-05-21 12:52 ./usr/bin/rsem-bam2readdepth
-rwxr-xr-x root/root 403004 2016-05-21 12:52 ./usr/bin/rsem-bam2wig
-rwxr-xr-x root/root 13824 2016-05-21 12:52 ./usr/bin/rsem-build-read-index
-rwxr-xr-x root/root 259648 2016-05-21 12:52 ./usr/bin/rsem-calculate-credibility-intervals
-rwxr-xr-x root/root 51083 2016-04-20 21:59 ./usr/bin/rsem-calculate-expression
-rwxr-xr-x root/root 3331 2016-04-20 21:59 ./usr/bin/rsem-control-fdr
-rwxr-xr-x root/root 75264 2016-05-21 12:52 ./usr/bin/rsem-extract-reference-transcripts
-rwxr-xr-x root/root 5605 2016-04-20 21:59 ./usr/bin/rsem-gen-transcript-plots
-rwxr-xr-x root/root 1979 2016-04-20 21:59 ./usr/bin/rsem-generate-data-matrix
-rwxr-xr-x root/root 3489 2016-04-20 21:59 ./usr/bin/rsem-generate-ngvector
-rwxr-xr-x root/root 398908 2016-05-21 12:52 ./usr/bin/rsem-get-unique
-rwxr-xr-x root/root 3300 2016-04-20 21:59 ./usr/bin/rsem-gff3-to-gtf
-rwxr-xr-x root/root 464448 2016-05-21 12:52 ./usr/bin/rsem-parse-alignments
-rwxr-xr-x root/root 5804 2016-04-20 21:59 ./usr/bin/rsem-plot-model
-rwxr-xr-x root/root 6735 2016-04-20 21:59 ./usr/bin/rsem-plot-transcript-wiggles
-rwxr-xr-x root/root 15863 2016-04-20 21:59 ./usr/bin/rsem-prepare-reference
-rwxr-xr-x root/root 34304 2016-05-21 12:52 ./usr/bin/rsem-preref
-rwxr-xr-x root/root 495 2016-04-20 21:59 ./usr/bin/rsem-refseq-extract-primary-assembly
-rwxr-xr-x root/root 6688 2016-04-20 21:59 ./usr/bin/rsem-run-ebseq
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-rwxr-xr-x root/root 403004 2016-05-21 12:52 ./usr/bin/rsem-sam-validator
-rwxr-xr-x root/root 407100 2016-05-21 12:52 ./usr/bin/rsem-scan-for-paired-end-reads
-rwxr-xr-x root/root 243264 2016-05-21 12:52 ./usr/bin/rsem-simulate-reads
-rwxr-xr-x root/root 75264 2016-05-21 12:52 ./usr/bin/rsem-synthesis-reference-transcripts
-rwxr-xr-x root/root 448060 2016-05-21 12:52 ./usr/bin/rsem-tbam2gbam
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/doc/rsem/
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-rw-r--r-- root/root 5043 2016-04-20 21:59 ./usr/share/doc/rsem/WHAT_IS_NEW.gz
-rw-r--r-- root/root 684 2016-05-15 10:49 ./usr/share/doc/rsem/changelog.Debian.gz
-rw-r--r-- root/root 1398 2016-04-20 21:59 ./usr/share/doc/rsem/cnt_file_description.txt
-rw-r--r-- root/root 3907 2016-05-14 18:38 ./usr/share/doc/rsem/copyright
-rw-r--r-- root/root 1544 2016-04-20 21:59 ./usr/share/doc/rsem/model_file_description.txt.gz
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 58 2016-05-15 10:32 ./usr/share/lintian/overrides/rsem
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/man/
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/man/man1/
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-rw-r--r-- root/root 504 2016-05-21 12:52 ./usr/share/man/man1/rsem-bam2wig.1.gz
-rw-r--r-- root/root 10551 2016-05-21 12:52 ./usr/share/man/man1/rsem-calculate-expression.1.gz
-rw-r--r-- root/root 2666 2016-05-21 12:52 ./usr/share/man/man1/rsem-control-fdr.1.gz
-rw-r--r-- root/root 3032 2016-05-21 12:52 ./usr/share/man/man1/rsem-generate-ngvector.1.gz
-rw-r--r-- root/root 394 2016-05-21 12:52 ./usr/share/man/man1/rsem-gff3-to-gtf.1.gz
-rw-r--r-- root/root 3268 2016-05-21 12:52 ./usr/share/man/man1/rsem-plot-transcript-wiggles.1.gz
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-rw-r--r-- root/root 1803 2016-05-21 12:52 ./usr/share/man/man1/rsem-simulate-reads.1.gz
drwxr-xr-x root/root 0 2016-05-21 12:52 ./usr/share/perl5/
-rw-r--r-- root/root 3562 2016-04-20 21:59 ./usr/share/perl5/rsem_perl_utils.pm
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 101772
Build-Time: 540
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 334
Job: rsem_1.2.30+dfsg-1
Machine Architecture: armhf
Package: rsem
Package-Time: 997
Source-Version: 1.2.30+dfsg-1
Space: 101772
Status: successful
Version: 1.2.30+dfsg-1
--------------------------------------------------------------------------------
Finished at 20160521-1253
Build needed 00:16:37, 101772k disc space