rsem →
1.2.23+dfsg-1 →
armhf → 2015-11-19 06:26:30
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-04
╔══════════════════════════════════════════════════════════════════════════════╗
║ rsem 1.2.23+dfsg-1 (armhf) 19 Nov 2015 06:16 ║
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Package: rsem
Version: 1.2.23+dfsg-1
Source Version: 1.2.23+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/rsem-Btmrwc/rsem-1.2.23+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/rsem-Btmrwc' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-ecc52b1b-bf7e-4db8-afab-7dc4a938ffc7' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8472 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.4 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
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...
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NOTICE: 'rsem' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/rsem.git
Need to get 137 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main rsem 1.2.23+dfsg-1 (dsc) [2026 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main rsem 1.2.23+dfsg-1 (tar) [129 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main rsem 1.2.23+dfsg-1 (diff) [5848 B]
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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-xZUWRK/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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Get:1 file: ./ Release.gpg [299 B]
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Ign file: ./ Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
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Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, libncurses5-dev, libbam-dev, libboost-dev, perl, bowtie | bowtie2
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, libncurses5-dev, libbam-dev, libboost-dev, perl, bowtie
dpkg-deb: building package 'sbuild-build-depends-rsem-dummy' in '/«BUILDDIR»/resolver-u2BeU6/apt_archive/sbuild-build-depends-rsem-dummy.deb'.
OK
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Get:1 file: ./ Release.gpg [299 B]
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Ign file: ./ Translation-en
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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 extra packages will be installed:
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 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:
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 libtinfo-dev libunistring0 libxml2 man-db
po-debconf sbuild-build-depends-rsem-dummy zlib1g-dev
0 upgraded, 28 newly installed, 0 to remove and 2 not upgraded.
Need to get 24.4 MB/24.4 MB of archives.
After this operation, 167 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-3 [1084 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.5-1 [975 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.25-2 [250 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.25-2 [61.2 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.6-1 [119 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-6 [7379 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.46.2-1 [2482 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.9-1 [129 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.6-1 [1393 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libarchive-zip-perl all 1.53-1 [97.3 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:20 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20151005 [817 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libbam-dev armhf 0.1.19-2 [109 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libboost1.58-dev armhf 1.58.0+dfsg-4 [6237 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libboost-dev armhf 1.58.0.1 [3472 B]
Get:24 http://172.17.0.1/private/ stretch-staging/main libtinfo-dev armhf 6.0+20151024-2 [65.8 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libncurses5-dev armhf 6.0+20151024-2 [154 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main bowtie armhf 1.0.0-5 [1320 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.19-22) ...
Setting up groff-base (1.22.3-3) ...
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 (1.4.1-1) ...
Setting up man-db (2.7.5-1) ...
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Setting up libffi6:armhf (3.2.1-3) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
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Setting up gettext-base (0.19.6-1) ...
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Setting up libxml2:armhf (2.9.2+zdfsg1-4) ...
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No schema files found: doing nothing.
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Setting up gettext (0.19.6-1) ...
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Setting up libarchive-zip-perl (1.53-1) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
Setting up libbam-dev (0.1.19-2) ...
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Setting up bowtie (1.0.0-5) ...
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-7 dpkg-dev_1.18.3 g++-4.9_4.9.3-5 g++-5_5.2.1-23+rpi1 gcc-4.9_4.9.3-5 gcc-5_5.2.1-23+rpi1 libc6-dev_2.19-22 libstdc++-4.9-dev_4.9.3-5 libstdc++-5-dev_5.2.1-23+rpi1 libstdc++6_5.2.1-23+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-7 bowtie_1.0.0-5 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-4.9_4.9.3-5 cpp-5_5.2.1-23+rpi1 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20151005 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1+rpi1 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 g++_4:5.2.1-4+rpi2 g++-4.9_4.9.3-5 g++-5_5.2.1-23+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1 gcc-4.9_4.9.3-5 gcc-4.9-base_4.9.3-5 gcc-5_5.2.1-23+rpi1 gcc-5-base_5.2.1-23+rpi1 gettext_0.19.6-1 gettext-base_0.19.6-1 gnupg_1.4.19-6 gpgv_1.4.19-6 grep_2.21-2 groff-base_1.22.3-3 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 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libarchive-zip-perl_1.53-1 libasan1_4.9.3-5 libasan2_5.2.1-23+rpi1 libatomic1_5.2.1-23+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libbam-dev_0.1.19-2 libblkid1_2.27.1-1 libboost-dev_1.58.0.1 libboost1.58-dev_1.58.0+dfsg-4 libbz2-1.0_1.0.6-8 libc-bin_2.19-22 libc-dev-bin_2.19-22 libc6_2.19-22 libc6-dev_2.19-22 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-23+rpi1 libcloog-isl4_0.18.3-1 libcomerr2_1.42.13-1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.10.2-1 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.110-1+rpi1 libdpkg-perl_1.18.3 libdrm2_2.4.65-3 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7 libgcc-4.9-dev_4.9.3-5 libgcc-5-dev_5.2.1-23+rpi1 libgcc1_1:5.2.1-23+rpi1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-1 libgmp10_2:6.0.0+dfsg-7+rpi1 libgomp1_5.2.1-23+rpi1 libgpg-error0_1.20-1 libicu55_55.1-6 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.07-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2 libncurses5-dev_6.0+20151024-2 libncursesw5_6.0+20151024-2 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-7.4 libpipeline1_1.4.1-1 libpng12-0_1.2.50-2+b2 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-1 libss2_1.42.13-1 libstdc++-4.9-dev_4.9.3-5 libstdc++-5-dev_5.2.1-23+rpi1 libstdc++6_5.2.1-23+rpi1 libsystemd0_227-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20151024-2 libtinfo5_6.0+20151024-2 libubsan0_5.2.1-23+rpi1 libudev1_227-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.2+zdfsg1-4 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 mawk_1.3.3-17 mount_2.27.1-1 multiarch-support_2.19-22 nano_2.4.2-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 po-debconf_1.0.18 procps_2:3.3.10-2 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_227-2 systemd-sysv_227-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 udev_227-2 util-linux_2.27.1-1 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 Thu Nov 5 18:33:57 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./rsem_1.2.23+dfsg-1.dsc
dpkg-source: info: extracting rsem in rsem-1.2.23+dfsg
dpkg-source: info: unpacking rsem_1.2.23+dfsg.orig.tar.gz
dpkg-source: info: unpacking rsem_1.2.23+dfsg-1.debian.tar.xz
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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-ecc52b1b-bf7e-4db8-afab-7dc4a938ffc7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package rsem
dpkg-buildpackage: source version 1.2.23+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build rsem-1.2.23+dfsg
dpkg-buildpackage: 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-1.2.23+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[1]: Leaving directory '/«BUILDDIR»/rsem-1.2.23+dfsg'
dh_clean -O--parallel
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_auto_configure -a -O--parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/rsem-1.2.23+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-1.2.23+dfsg'
g++ -Wl,-z,relro -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 -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
g++ -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++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -c -I. parseIt.cpp
g++ -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++ -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++ -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++ -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++ -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++ -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++ -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++ -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++ -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++ -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++ -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++ -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o rsem-run-gibbs Gibbs.o -lpthread
g++ -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o rsem-calculate-credibility-intervals calcCI.o -lpthread
g++ -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
g++ -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
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++ -Wl,-z,relro -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
g++ -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o rsem-simulate-reads simulation.o
make[2]: Leaving directory '/«BUILDDIR»/rsem-1.2.23+dfsg'
make[1]: Leaving directory '/«BUILDDIR»/rsem-1.2.23+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-1.2.23+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-1.2.23+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-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-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-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-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-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-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: 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-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-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-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-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-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-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
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
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' in '../rsem_1.2.23+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../rsem_1.2.23+dfsg-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build rsem-1.2.23+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151119-0626
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
rsem_1.2.23+dfsg-1_armhf.changes:
─────────────────────────────────
Format: 1.8
Date: Thu, 05 Nov 2015 19:28:01 +0100
Source: rsem
Binary: rsem
Architecture: armhf
Version: 1.2.23+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <crusoe@ucdavis.edu>
Description:
rsem - RNA-Seq by Expectation-Maximization
Closes: 803550
Changes:
rsem (1.2.23+dfsg-1) unstable; urgency=medium
.
[ Michael R. Crusoe ]
* New upstream release
.
[ Andreas Tille ]
* Build-Depends: bowtie to enable builds only on those architectures
where bowtie is available
Closes: #803550
Checksums-Sha1:
3446ef3cbcb3086d25276305fb90649b6462ed11 393032 rsem_1.2.23+dfsg-1_armhf.deb
Checksums-Sha256:
55050d195f451d7c83e20f4a71c7b12a5435ea6b9ab02176c449ebc937ad227a 393032 rsem_1.2.23+dfsg-1_armhf.deb
Files:
9f9bcb0f93ae950785cdfb8aaaa5f3e1 393032 science optional rsem_1.2.23+dfsg-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
rsem_1.2.23+dfsg-1_armhf.deb
────────────────────────────
new debian package, version 2.0.
size 393032 bytes: control archive=2343 bytes.
1535 bytes, 27 lines control
2810 bytes, 41 lines md5sums
Package: rsem
Version: 1.2.23+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2242
Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), perl, r-base-core, bowtie | bowtie2
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.
drwxr-xr-x root/root 0 2015-11-19 06:25 ./
drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/
drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/bin/
-rwxr-xr-x root/root 4307 2015-11-19 06:21 ./usr/bin/convert-sam-for-rsem
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-rwxr-xr-x root/root 4898 2015-10-19 23:41 ./usr/bin/rsem-plot-model
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-rwxr-xr-x root/root 158788 2015-11-19 06:25 ./usr/bin/rsem-tbam2gbam
drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/share/
drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/share/doc/rsem/
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-rw-r--r-- root/root 4192 2015-10-19 23:41 ./usr/share/doc/rsem/WHAT_IS_NEW.gz
-rw-r--r-- root/root 298 2015-11-05 18:31 ./usr/share/doc/rsem/changelog.Debian.gz
-rw-r--r-- root/root 1398 2015-10-19 23:41 ./usr/share/doc/rsem/cnt_file_description.txt
-rw-r--r-- root/root 1089 2015-11-05 18:31 ./usr/share/doc/rsem/copyright
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drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/share/lintian/
drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 300 2015-11-05 18:31 ./usr/share/lintian/overrides/rsem
drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/share/man/
drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/share/man/man1/
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-rw-r--r-- root/root 4917 2015-11-19 06:25 ./usr/share/man/man1/rsem-prepare-reference.1.gz
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drwxr-xr-x root/root 0 2015-11-19 06:25 ./usr/share/perl5/
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 29096
Build-Time: 278
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 237
Job: rsem_1.2.23+dfsg-1
Machine Architecture: armhf
Package: rsem
Package-Time: 575
Source-Version: 1.2.23+dfsg-1
Space: 29096
Status: successful
Version: 1.2.23+dfsg-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20151119-0626
Build needed 00:09:35, 29096k disc space