rsem →
1.3.0+dfsg-2 →
armhf → 2018-05-27 05:30:13
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| rsem 1.3.0+dfsg-2 (armhf) Sun, 27 May 2018 05:13:48 +0000 |
+==============================================================================+
Package: rsem
Version: 1.3.0+dfsg-2
Source Version: 1.3.0+dfsg-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-497ff537-8c57-45e7-a578-ffa5559d546e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
Fetched 23.3 MB in 26s (890 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
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://salsa.debian.org/med-team/rsem.git
Please use:
git clone https://salsa.debian.org/med-team/rsem.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 35.9 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main rsem 1.3.0+dfsg-2 (dsc) [2100 B]
Get:2 http://172.17.0.1/private buster-staging/main rsem 1.3.0+dfsg-2 (tar) [274 kB]
Get:3 http://172.17.0.1/private buster-staging/main rsem 1.3.0+dfsg-2 (diff) [35.7 MB]
Fetched 35.9 MB in 3s (10.3 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/rsem-gGbu3V/rsem-1.3.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/rsem-gGbu3V' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-lfIlio/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-lfIlio/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-lfIlio/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ Packages [429 B]
Fetched 2105 B in 1s (2959 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 68 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13964 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), zlib1g-dev, libncurses5-dev, libboost-dev, perl, python, help2man, libhts-dev, bowtie | bowtie2
Filtered Build-Depends: debhelper (>= 11~), zlib1g-dev, libncurses5-dev, libboost-dev, perl, python, help2man, libhts-dev, bowtie
dpkg-deb: building package 'sbuild-build-depends-rsem-dummy' in '/<<BUILDDIR>>/resolver-lfIlio/apt_archive/sbuild-build-depends-rsem-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-rsem-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ Sources [537 B]
Get:5 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ Packages [614 B]
Fetched 2484 B in 1s (3437 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install rsem build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bowtie bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libboost-dev
libboost1.62-dev libbsd0 libcroco3 libcurl3-gnutls libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libhts-dev libhts2 libicu-le-hb0 libicu60
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
libmagic1 libncurses-dev libncurses5-dev libncurses6 libncursesw6
libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1 libtimedate-perl
libtinfo6 libtool libxml2 m4 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal zlib1g 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 libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user
liblzma-doc ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk
python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bowtie bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libboost-dev
libboost1.62-dev libbsd0 libcroco3 libcurl3-gnutls libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libhts-dev libhts2 libicu-le-hb0 libicu60
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
libmagic1 libncurses-dev libncurses5-dev libncurses6 libncursesw6
libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1 libtimedate-perl
libtinfo6 libtool libxml2 m4 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal sbuild-build-depends-rsem-dummy
zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 67 newly installed, 0 to remove and 67 not upgraded.
Need to get 34.5 MB/36.3 MB of archives.
After this operation, 213 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-lfIlio/apt_archive ./ sbuild-build-depends-rsem-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.3 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-1 [393 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-1 [1077 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15~rc1-1 [41.1 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20180210-3 [307 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20180210-3 [103 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-1 [1841 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-1 [298 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15~rc1-1 [20.5 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15~rc1-1 [155 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-2 [234 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-2 [106 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-2 [64.7 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.7.6-1+b1 [799 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-6.1+b1 [602 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.2 [994 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.6 [169 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-5.1 [7003 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:46 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.1-1 [51.4 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.60.0-1 [279 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libncurses6 armhf 6.1+20180210-3 [78.3 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-3 [278 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-3 [924 B]
Get:55 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf bowtie armhf 1.0.0-5 [1320 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.33-2) ...
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Setting up libgraphite2-3:armhf (1.3.11-2) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
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Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up help2man (1.47.6) ...
Setting up libboost-dev:armhf (1.62.0.1+b8) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
Setting up bsdmainutils (11.1.2) ...
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 libncurses6:armhf (6.1+20180210-3) ...
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Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.041-1) ...
Setting up libncursesw6:armhf (6.1+20180210-3) ...
Setting up libharfbuzz0b:armhf (1.7.6-1+b1) ...
Setting up autoconf (2.69-11) ...
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Setting up libkrb5support0:armhf (1.16-2) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libpython2.7-stdlib:armhf (2.7.15-1) ...
Setting up libtool (2.4.6-2.1) ...
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Setting up libkrb5-3:armhf (1.16-2) ...
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Setting up libhts2:armhf (1.7-2) ...
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Setting up dh-strip-nondeterminism (0.041-1) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-6.1+b1) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up gettext (0.19.8.1-6) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.3.2) ...
Setting up sbuild-build-depends-rsem-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bowtie_1.0.0-5 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.3.2 debianutils_4.8.4 dh-autoreconf_19 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 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_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-6-base_6.4.0-12+rpi1 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 help2man_1.47.6 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libblkid1_2.31.1-0.5 libboost-dev_1.62.0.1+b8 libboost1.62-dev_1.62.0+dfsg-5.1 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.60.0-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libelf1_0.170-0.4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libgraphite2-3_1.3.11-2 libgssapi-krb5-2_1.16-2 libharfbuzz0b_1.7.6-1+b1 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.1.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180210-3 libncurses5_6.1-1 libncurses5-dev_6.1+20180210-3 libncurses6_6.1+20180210-3 libncursesw5_6.1-1 libncursesw6_6.1+20180210-3 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.5-3 libnss-systemd_238-4 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libpsl5_0.20.1-1 libpython-stdlib_2.7.15~rc1-1 libpython2.7-minimal_2.7.15-1 libpython2.7-stdlib_2.7.15-1 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssh2-1_1.8.0-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtinfo6_6.1+20180210-3 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1+b1 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.60 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 python_2.7.15~rc1-1 python-minimal_2.7.15~rc1-1 python2.7_2.7.15-1 python2.7-minimal_2.7.15-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rsem-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-4 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri May 25 12:08:12 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./rsem_1.3.0+dfsg-2.dsc
dpkg-source: info: extracting rsem in /<<BUILDDIR>>/rsem-1.3.0+dfsg
dpkg-source: info: unpacking rsem_1.3.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking rsem_1.3.0+dfsg-2.debian.tar.xz
dpkg-source: info: applying hardening
dpkg-source: info: applying use_debian_packaged_samtools.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-497ff537-8c57-45e7-a578-ffa5559d546e
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 1.3.0+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build rsem-1.3.0+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.3.0+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 EBSeq && make clean
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.3.0+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-1.3.0+dfsg/EBSeq'
cd pRSEM && make clean
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.3.0+dfsg/pRSEM'
rm -fr bigWigSummary RLib filterSam2Bed *.pyc
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.0+dfsg/pRSEM'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.0+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.3.0+dfsg'
dh_auto_build -- BOOST=/usr/include prefix=debian/tmp
make -j4 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.3.0+dfsg'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp
In file included from SamParser.h:13:0,
from parseIt.cpp:27:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from utils.h:12,
from parseIt.cpp:13:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = SingleHit; _Alloc = std::allocator<SingleHit>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<SingleHit, std::allocator<SingleHit> >::iterator {aka __gnu_cxx::__normal_iterator<SingleHit*, std::vector<SingleHit, std::allocator<SingleHit> > >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PairedEndHit; _Alloc = std::allocator<PairedEndHit>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<PairedEndHit, std::allocator<PairedEndHit> >::iterator {aka __gnu_cxx::__normal_iterator<PairedEndHit*, std::vector<PairedEndHit, std::allocator<PairedEndHit> > >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from utils.h:12,
from parseIt.cpp:13:
/usr/include/c++/7/bits/stl_vector.h: In function 'void parseIt(SamParser*) [with ReadType = SingleRead; HitType = SingleHit]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SingleHit*, std::vector<SingleHit, std::allocator<SingleHit> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
}
^
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from utils.h:12,
from parseIt.cpp:13:
/usr/include/c++/7/bits/stl_vector.h: In function 'void parseIt(SamParser*) [with ReadType = SingleReadQ; HitType = SingleHit]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SingleHit*, std::vector<SingleHit, std::allocator<SingleHit> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
}
^
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from utils.h:12,
from parseIt.cpp:13:
/usr/include/c++/7/bits/stl_vector.h: In function 'void parseIt(SamParser*) [with ReadType = PairedEndRead; HitType = PairedEndHit]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PairedEndHit*, std::vector<PairedEndHit, std::allocator<PairedEndHit> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
}
^
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp
In file included from /usr/include/c++/7/vector:64:0,
from utils.h:12,
from parseIt.cpp:13:
/usr/include/c++/7/bits/stl_vector.h: In function 'void parseIt(SamParser*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PairedEndHit*, std::vector<PairedEndHit, std::allocator<PairedEndHit> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
}
^
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
parseIt.cpp:152:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp
In file included from BamConverter.h:12:0,
from tbam2gbam.cpp:8:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
In file included from tbam2gbam.cpp:8:0:
BamConverter.h: In constructor 'BamConverter::BamConverter(const char*, const char*, const char*, Transcripts&, int, const string&)':
BamConverter.h:70:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(out, out_header);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
BamConverter.h: In member function 'void BamConverter::process()':
BamConverter.h:137:15: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, b);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BamConverter.h:138:29: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
if (isPaired) sam_write1(out, out_header, b2);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
BamConverter.h: In member function 'void BamConverter::writeCollapsedLines()':
BamConverter.h:208:14: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, tmp_b);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
BamConverter.h:212:15: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, tmp_b2);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp
In file included from BamWriter.h:14:0,
from EM.cpp:45:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp
In file included from EM.cpp:45:0:
BamWriter.h: In constructor 'BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)':
BamWriter.h:70:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(out, out_header);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
BamWriter.h: In member function 'void BamWriter::work(HitWrapper<SingleHit>)':
BamWriter.h:101:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, b);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BamWriter.h: In member function 'void BamWriter::work(HitWrapper<PairedEndHit>)':
BamWriter.h:136:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, b);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BamWriter.h:137:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, b2);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from wiggle.cpp:8:0:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp
In file included from getUnique.cpp:10:0:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp
getUnique.cpp: In function 'void output()':
getUnique.cpp:29:52: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
getUnique.cpp: In function 'int main(int, char**)':
getUnique.cpp:45:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(out, header);
~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp
In file included from samValidator.cpp:11:0:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
samValidator.cpp: In function 'bool check_read(bam1_t*, bam_hdr_t*)':
samValidator.cpp:28:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < b->core.n_cigar; ++i) {
~~^~~~~~~~~~~~~~~~~
samValidator.cpp:45:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->core.pos < 0 || bam_endpos(b) > header->target_len[b->core.tid]) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samValidator.cpp: In function 'int main(int, char**)':
samValidator.cpp:143:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
isValid = tb->core.pos >= 0 && tb->core.pos + abs(tb->core.isize) <= header->target_len[tb->core.tid];
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from scanForPairedEndReads.cpp:11:0:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
scanForPairedEndReads.cpp: In function 'int main(int, char**)':
scanForPairedEndReads.cpp:66:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(out, header);
~~~~~~~~~~~~~^~~~~~~~~~~~~
scanForPairedEndReads.cpp:94:65: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
for (size_t i = 0; i < arr_both.size(); i++) { sam_write1(out, header, arr_both[i]); bam_destroy1(arr_both[i]); }
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:100:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back();
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:101:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back();
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:104:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back();
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:105:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back();
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:108:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back();
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:109:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back();
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:114:18: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back();
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:118:16: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, b);
~~~~~~~~~~^~~~~~~~~~~~~~~~
scanForPairedEndReads.cpp:120:18: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, header, b);
~~~~~~~~~~^~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp
g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o
g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o
g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o
g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o
g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz
In file included from /usr/include/c++/7/vector:69:0,
from EM.cpp:8:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from EM.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, std::vector<_Tp, _Alloc>::value_type) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void* E_STEP(void*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void* E_STEP(void*) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void* E_STEP(void*) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void* E_STEP(void*) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from EM.cpp:8:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = SingleHit; _Alloc = std::allocator<SingleHit>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<SingleHit, std::allocator<SingleHit> >::iterator {aka __gnu_cxx::__normal_iterator<SingleHit*, std::vector<SingleHit, std::allocator<SingleHit> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from EM.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool HitContainer<HitType>::read(std::istream&) [with HitType = SingleHit]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SingleHit*, std::vector<SingleHit, std::allocator<SingleHit> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void init(ReadReader<ReadType>**&, HitContainer<HitType>**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void init(ReadReader<ReadType>**&, HitContainer<HitType>**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from EM.cpp:8:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PairedEndHit; _Alloc = std::allocator<PairedEndHit>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<PairedEndHit, std::allocator<PairedEndHit> >::iterator {aka __gnu_cxx::__normal_iterator<PairedEndHit*, std::vector<PairedEndHit, std::allocator<PairedEndHit> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from EM.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool HitContainer<HitType>::read(std::istream&) [with HitType = PairedEndHit]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PairedEndHit*, std::vector<PairedEndHit, std::allocator<PairedEndHit> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void init(ReadReader<ReadType>**&, HitContainer<HitType>**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void init(ReadReader<ReadType>**&, HitContainer<HitType>**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from Gibbs.cpp:7:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = Item; _Alloc = std::allocator<Item>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<Item>::iterator {aka __gnu_cxx::__normal_iterator<Item*, std::vector<Item> >}' changed in GCC 7.1
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz
In file included from /usr/include/c++/7/vector:64:0,
from Gibbs.cpp:7:
/usr/include/c++/7/bits/stl_vector.h: In function 'void load_data(char*, char*, char*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Item*, std::vector<Item> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.0+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="1.3.0+dfsg" \
--name 'Convert GFF3 files to GTF files.' > \
debian/rsem-gff3-to-gtf.1
help2man ./rsem-bam2wig --no-info --version-string="1.3.0+dfsg" \
--name 'Convert BAM files to wiggle files.' > \
debian/rsem-bam2wig.1
help2man ./rsem-simulate-reads --no-info --version-string="1.3.0+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-1.3.0+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.3.0+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="/usr"
make -j4 install DESTDIR=/<<BUILDDIR>>/rsem-1.3.0\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.3.0+dfsg'
install --strip-program=true -p rsem-extract-reference-transcripts /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-calculate-credibility-intervals ;
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install --strip-program=true -p rsem-prepare-reference /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/convert-sam-for-rsem ;
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install: WARNING: ignoring --strip-program option as -s option was not specified
install --strip-program=true -p -m 644 rsem_perl_utils.pm /<<BUILDDIR>>/rsem-1.3.0+dfsg/debian/rsem/usr/bin/rsem_perl_utils.pm
install: WARNING: ignoring --strip-program option as -s option was not specified
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.0+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-simulate-reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-synthesis-reference-transcripts contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-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-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-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-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-sam-validator contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-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-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-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-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-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-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-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-extract-reference-transcripts contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/rsem/usr/bin/rsem-simulate-reads debian/rsem/usr/bin/rsem-synthesis-reference-transcripts debian/rsem/usr/bin/rsem-build-read-index debian/rsem/usr/bin/rsem-bam2wig debian/rsem/usr/bin/rsem-calculate-credibility-intervals debian/rsem/usr/bin/rsem-parse-alignments debian/rsem/usr/bin/rsem-sam-validator debian/rsem/usr/bin/rsem-scan-for-paired-end-reads debian/rsem/usr/bin/rsem-run-em debian/rsem/usr/bin/rsem-bam2readdepth debian/rsem/usr/bin/rsem-preref debian/rsem/usr/bin/rsem-run-gibbs debian/rsem/usr/bin/rsem-tbam2gbam debian/rsem/usr/bin/rsem-get-unique debian/rsem/usr/bin/rsem-extract-reference-transcripts were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/rsem/usr/bin/rsem-bam2wig debian/rsem/usr/bin/rsem-parse-alignments debian/rsem/usr/bin/rsem-sam-validator debian/rsem/usr/bin/rsem-scan-for-paired-end-reads debian/rsem/usr/bin/rsem-run-em debian/rsem/usr/bin/rsem-bam2readdepth debian/rsem/usr/bin/rsem-tbam2gbam debian/rsem/usr/bin/rsem-get-unique were not linked against libz.so.1 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.0+dfsg-2_armhf.deb'.
dpkg-deb: building package 'rsem' in '../rsem_1.3.0+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../rsem_1.3.0+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build rsem-1.3.0+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-05-27T05:29:34Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
rsem_1.3.0+dfsg-2_armhf.changes:
--------------------------------
Format: 1.8
Date: Fri, 25 May 2018 13:56:22 +0200
Source: rsem
Binary: rsem
Architecture: armhf
Version: 1.3.0+dfsg-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Katerina Kalou <aik.kalou@gmail.com>
Description:
rsem - RNA-Seq by Expectation-Maximization
Closes: 847569 890782
Changes:
rsem (1.3.0+dfsg-2) unstable; urgency=medium
.
[ Katerina Kalou ]
* Team upload.
* Add autopkgtest
Closes: #890782
.
[ Andreas Tille ]
* Upload to unstable
Closes: #847569
* Remove unused lintian-override
* Drop unused License specification
* Point Vcs-fields to Salsa
* Standards-Version: 4.1.4
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
rsem-dbgsym_1.3.0+dfsg-2_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 3841356 bytes: control archive=1240 bytes.
943 bytes, 12 lines control
1590 bytes, 15 lines md5sums
Package: rsem-dbgsym
Source: rsem
Version: 1.3.0+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4161
Depends: rsem (= 1.3.0+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for rsem
Build-Ids: 146d186ee80b3b4e31c69e69f5546bed862ebab7 266915f80f360734a6ca44dbe2131f8369297177 373f2391d445300202c1685c913f270f295a17f1 65e7c3853fda4d934e56abb35a8990f9e2290d05 6982643f4ca13aea1323f1a714a5e7f2a82cd32f 6d98efe2e607cd4c2663e4498e4e1d3d0e6595a9 74c4d4f9e3b978bd732f7afbd97b3b2f76e7e439 793c37f2a8895adfe63db6f9cce6efdd195688a8 8903b49e37b99b5132168b0ecd1a02fb4d73ae18 9ba319b74539b8a933001f31581abc04a58dd464 bc8efa27a2e03454d44592981050fd66d398c6ff cc957c358e9360b392833f5a30f45b318dfc1a22 da5ce343045f04c00e7858321cc8b59f84d6f9ea e2e15f7f58686c96fe29719c0ef92ab1678791d6 ed18a1204243d7b781a2b305a1571f3202ffdb9d
drwxr-xr-x root/root 0 2018-05-25 11:56 ./
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/14/
-rw-r--r-- root/root 173452 2018-05-25 11:56 ./usr/lib/debug/.build-id/14/6d186ee80b3b4e31c69e69f5546bed862ebab7.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/26/
-rw-r--r-- root/root 165156 2018-05-25 11:56 ./usr/lib/debug/.build-id/26/6915f80f360734a6ca44dbe2131f8369297177.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/37/
-rw-r--r-- root/root 176400 2018-05-25 11:56 ./usr/lib/debug/.build-id/37/3f2391d445300202c1685c913f270f295a17f1.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/65/
-rw-r--r-- root/root 677260 2018-05-25 11:56 ./usr/lib/debug/.build-id/65/e7c3853fda4d934e56abb35a8990f9e2290d05.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/69/
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drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/6d/
-rw-r--r-- root/root 157588 2018-05-25 11:56 ./usr/lib/debug/.build-id/6d/98efe2e607cd4c2663e4498e4e1d3d0e6595a9.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/74/
-rw-r--r-- root/root 121004 2018-05-25 11:56 ./usr/lib/debug/.build-id/74/c4d4f9e3b978bd732f7afbd97b3b2f76e7e439.debug
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-rw-r--r-- root/root 296708 2018-05-25 11:56 ./usr/lib/debug/.build-id/79/3c37f2a8895adfe63db6f9cce6efdd195688a8.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/89/
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drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/9b/
-rw-r--r-- root/root 463508 2018-05-25 11:56 ./usr/lib/debug/.build-id/9b/a319b74539b8a933001f31581abc04a58dd464.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/bc/
-rw-r--r-- root/root 464048 2018-05-25 11:56 ./usr/lib/debug/.build-id/bc/8efa27a2e03454d44592981050fd66d398c6ff.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/cc/
-rw-r--r-- root/root 256756 2018-05-25 11:56 ./usr/lib/debug/.build-id/cc/957c358e9360b392833f5a30f45b318dfc1a22.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/da/
-rw-r--r-- root/root 261812 2018-05-25 11:56 ./usr/lib/debug/.build-id/da/5ce343045f04c00e7858321cc8b59f84d6f9ea.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/e2/
-rw-r--r-- root/root 43844 2018-05-25 11:56 ./usr/lib/debug/.build-id/e2/e15f7f58686c96fe29719c0ef92ab1678791d6.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/lib/debug/.build-id/ed/
-rw-r--r-- root/root 436996 2018-05-25 11:56 ./usr/lib/debug/.build-id/ed/18a1204243d7b781a2b305a1571f3202ffdb9d.debug
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-05-25 11:56 ./usr/share/doc/rsem-dbgsym -> rsem
rsem_1.3.0+dfsg-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 36011968 bytes: control archive=2544 bytes.
1557 bytes, 27 lines control
3346 bytes, 48 lines md5sums
Package: rsem
Version: 1.3.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 36530
Depends: libc6 (>= 2.15), libgcc1 (>= 1:3.5), libhts2 (>= 1.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), perl, r-base-core, bowtie | bowtie2, python
Suggests: r-bioc-ebseq
Section: science
Priority: optional
Homepage: http://deweylab.biostat.wisc.edu/rsem/
Description: RNA-Seq by Expectation-Maximization
RSEM is a software package for estimating gene and isoform expression
levels from RNA-Seq data. The RSEM package provides an user-friendly
interface, supports threads for parallel computation of the EM
algorithm, single-end and paired-end read data, quality scores,
variable-length reads and RSPD estimation. In addition, it provides
posterior mean and 95% credibility interval estimates for expression
levels. For visualization, It can generate BAM and Wiggle files in both
transcript-coordinate and genomic-coordinate. Genomic-coordinate files
can be visualized by both UCSC Genome browser and Broad Institute’s
Integrative Genomics Viewer (IGV). Transcript-coordinate files can be
visualized by IGV. RSEM also has its own scripts to generate transcript
read depth plots in pdf format. The unique feature of RSEM is, the read
depth plots can be stacked, with read depth contributed to unique reads
shown in black and contributed to multi-reads shown in red. In addition,
models learned from data can also be visualized. Last but not least,
RSEM contains a simulator.
drwxr-xr-x root/root 0 2018-05-25 11:56 ./
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/bin/
-rwxr-xr-x root/root 2917 2016-10-02 14:34 ./usr/bin/convert-sam-for-rsem
-rwxr-xr-x root/root 791 2016-10-02 14:34 ./usr/bin/extract-transcript-to-gene-map-from-trinity
-rwxr-xr-x root/root 42508 2018-05-25 11:56 ./usr/bin/rsem-bam2readdepth
-rwxr-xr-x root/root 42508 2018-05-25 11:56 ./usr/bin/rsem-bam2wig
-rwxr-xr-x root/root 13832 2018-05-25 11:56 ./usr/bin/rsem-build-read-index
-rwxr-xr-x root/root 210452 2018-05-25 11:56 ./usr/bin/rsem-calculate-credibility-intervals
-rwxr-xr-x root/root 72655 2016-10-02 14:34 ./usr/bin/rsem-calculate-expression
-rwxr-xr-x root/root 3331 2016-10-02 14:34 ./usr/bin/rsem-control-fdr
-rwxr-xr-x root/root 71176 2018-05-25 11:56 ./usr/bin/rsem-extract-reference-transcripts
-rwxr-xr-x root/root 5605 2016-10-02 14:34 ./usr/bin/rsem-gen-transcript-plots
-rwxr-xr-x root/root 1979 2016-10-02 14:34 ./usr/bin/rsem-generate-data-matrix
-rwxr-xr-x root/root 3489 2016-10-02 14:34 ./usr/bin/rsem-generate-ngvector
-rwxr-xr-x root/root 42508 2018-05-25 11:56 ./usr/bin/rsem-get-unique
-rwxr-xr-x root/root 9350 2016-10-02 14:34 ./usr/bin/rsem-gff3-to-gtf
-rwxr-xr-x root/root 103948 2018-05-25 11:56 ./usr/bin/rsem-parse-alignments
-rwxr-xr-x root/root 5804 2016-10-02 14:34 ./usr/bin/rsem-plot-model
-rwxr-xr-x root/root 6735 2016-10-02 14:34 ./usr/bin/rsem-plot-transcript-wiggles
-rwxr-xr-x root/root 21122 2016-10-02 14:34 ./usr/bin/rsem-prepare-reference
-rwxr-xr-x root/root 30216 2018-05-25 11:56 ./usr/bin/rsem-preref
-rwxr-xr-x root/root 495 2016-10-02 14:34 ./usr/bin/rsem-refseq-extract-primary-assembly
-rwxr-xr-x root/root 300568 2018-05-25 11:56 ./usr/bin/rsem-run-em
-rwxr-xr-x root/root 202260 2018-05-25 11:56 ./usr/bin/rsem-run-gibbs
-rwxr-xr-x root/root 42508 2018-05-25 11:56 ./usr/bin/rsem-sam-validator
-rwxr-xr-x root/root 46604 2018-05-25 11:56 ./usr/bin/rsem-scan-for-paired-end-reads
-rwxr-xr-x root/root 198164 2018-05-25 11:56 ./usr/bin/rsem-simulate-reads
-rwxr-xr-x root/root 71176 2018-05-25 11:56 ./usr/bin/rsem-synthesis-reference-transcripts
-rwxr-xr-x root/root 87564 2018-05-25 11:56 ./usr/bin/rsem-tbam2gbam
-rwxr-xr-x root/root 3749 2016-10-02 14:34 ./usr/bin/rsem_perl_utils.pm
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/doc/rsem/
-rw-r--r-- root/root 11183 2016-10-02 14:34 ./usr/share/doc/rsem/README.md.gz
-rw-r--r-- root/root 431 2018-05-25 11:56 ./usr/share/doc/rsem/README.test
-rw-r--r-- root/root 5423 2016-10-02 14:34 ./usr/share/doc/rsem/WHAT_IS_NEW.gz
-rw-r--r-- root/root 996 2018-05-25 11:56 ./usr/share/doc/rsem/changelog.Debian.gz
-rw-r--r-- root/root 1398 2016-10-02 14:34 ./usr/share/doc/rsem/cnt_file_description.txt
-rw-r--r-- root/root 1169 2018-05-25 11:56 ./usr/share/doc/rsem/copyright
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/doc/rsem/examples/
-rw-r--r-- root/root 35665587 2018-05-25 11:56 ./usr/share/doc/rsem/examples/mouse_ref_building_from_transcripts.tar.gz
-rw-r--r-- root/root 1544 2016-10-02 14:34 ./usr/share/doc/rsem/model_file_description.txt.gz
-rw-r--r-- root/root 415 2018-05-25 11:56 ./usr/share/doc/rsem/run-unit-test
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/man/
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/man/man1/
-rw-r--r-- root/root 2505 2018-05-25 11:56 ./usr/share/man/man1/convert-sam-for-rsem.1.gz
-rw-r--r-- root/root 504 2018-05-25 11:56 ./usr/share/man/man1/rsem-bam2wig.1.gz
-rw-r--r-- root/root 13710 2018-05-25 11:56 ./usr/share/man/man1/rsem-calculate-expression.1.gz
-rw-r--r-- root/root 2632 2018-05-25 11:56 ./usr/share/man/man1/rsem-control-fdr.1.gz
-rw-r--r-- root/root 3002 2018-05-25 11:56 ./usr/share/man/man1/rsem-generate-ngvector.1.gz
-rw-r--r-- root/root 468 2018-05-25 11:56 ./usr/share/man/man1/rsem-gff3-to-gtf.1.gz
-rw-r--r-- root/root 3239 2018-05-25 11:56 ./usr/share/man/man1/rsem-plot-transcript-wiggles.1.gz
-rw-r--r-- root/root 5820 2018-05-25 11:56 ./usr/share/man/man1/rsem-prepare-reference.1.gz
-rw-r--r-- root/root 3654 2018-05-25 11:56 ./usr/share/man/man1/rsem-run-ebseq.1.gz
-rw-r--r-- root/root 1802 2018-05-25 11:56 ./usr/share/man/man1/rsem-simulate-reads.1.gz
drwxr-xr-x root/root 0 2018-05-25 11:56 ./usr/share/perl5/
-rw-r--r-- root/root 3749 2016-10-02 14:34 ./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: 149928
Build-Time: 381
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 511
Job: rsem_1.3.0+dfsg-2
Machine Architecture: armhf
Package: rsem
Package-Time: 946
Source-Version: 1.3.0+dfsg-2
Space: 149928
Status: successful
Version: 1.3.0+dfsg-2
--------------------------------------------------------------------------------
Finished at 2018-05-27T05:29:34Z
Build needed 00:15:46, 149928k disc space