rsem →
1.3.2+dfsg-1 →
armhf → 2019-07-15 13:06:53
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| rsem 1.3.2+dfsg-1 (armhf) Mon, 15 Jul 2019 12:48:07 +0000 |
+==============================================================================+
Package: rsem
Version: 1.3.2+dfsg-1
Source Version: 1.3.2+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-bc5b264c-c81b-417f-b9ab-3f003d1efd22' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.4 MB in 29s (834 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 bullseye-staging/main rsem 1.3.2+dfsg-1 (dsc) [2104 B]
Get:2 http://172.17.0.1/private bullseye-staging/main rsem 1.3.2+dfsg-1 (tar) [275 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main rsem 1.3.2+dfsg-1 (diff) [35.7 MB]
Fetched 35.9 MB in 28s (1288 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/rsem-mtwvlb/rsem-1.3.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/rsem-mtwvlb' 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-6R9BJT/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-6R9BJT/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-6R9BJT/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-6R9BJT/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2829 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 24 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-6R9BJT/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 ... 12050 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 (>= 12~), zlib1g-dev, libncurses5-dev, libboost-dev, perl, python, help2man, libhts-dev, bowtie | bowtie2
Filtered Build-Depends: debhelper (>= 12~), zlib1g-dev, libncurses5-dev, libboost-dev, perl, python, help2man, libhts-dev, bowtie
dpkg-deb: building package 'sbuild-build-depends-rsem-dummy' in '/<<BUILDDIR>>/resolver-6R9BJT/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-6R9BJT/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ Packages [619 B]
Fetched 2492 B in 1s (3016 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
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
libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts-dev libhts2 libicu63 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libncurses-dev
libncurses5-dev libncurses6 libnghttp2-14 libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libssl1.1 libtinfo5 libtool libuchardet0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2
python2-minimal python2.7 python2.7-minimal sensible-utils 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 libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-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-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates 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
libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts-dev libhts2 libicu63 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libncurses-dev
libncurses5-dev libncurses6 libnghttp2-14 libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libssl1.1 libtinfo5 libtool libuchardet0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2
python2-minimal python2.7 python2.7-minimal sbuild-build-depends-rsem-dummy
sensible-utils zlib1g-dev
0 upgraded, 69 newly installed, 0 to remove and 24 not upgraded.
Need to get 39.9 MB of archives.
After this operation, 231 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-6R9BJT/apt_archive ./ sbuild-build-depends-rsem-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.9.1-2 [104 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20181013-2 [309 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-minimal armhf 2.7.16-2 [395 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python2.7-minimal armhf 2.7.16-2 [1093 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python-minimal armhf 2.7.16-1 [21.0 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1c-1 [1259 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.62 [37.2 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.6-2 [77.1 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-stdlib armhf 2.7.16-2 [1844 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python2.7 armhf 2.7.16-2 [305 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python2 armhf 2.7.16-1 [41.6 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python armhf 2.7.16-1 [22.8 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.35-4 [242 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.35-4 [110 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.35-4 [65.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.58.3-2 [1077 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
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Get:44 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20181013-2 [78.6 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.1.1 [1016 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.8 [176 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-3 [62.2 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-3 [118 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-3 [317 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-3 [135 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.37.0-1 [72.2 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.64.0-4 [291 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.2-1 [48.4 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-11 [255 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-11 [4286 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.1+20181013-2 [278 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.1+20181013-2 [940 B]
Get:69 http://172.17.0.1/private bullseye-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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No schema files found: doing nothing.
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Setting up libkrb5support0:armhf (1.17-3) ...
Setting up libpython2.7-stdlib:armhf (2.7.16-2) ...
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Setting up libncurses-dev:armhf (6.1+20181013-2) ...
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Setting up libpython2-stdlib:armhf (2.7.16-1) ...
Setting up m4 (1.4.18-2) ...
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Setting up libpython-stdlib:armhf (2.7.16-1) ...
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
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Setting up libcroco3:armhf (0.6.12-3) ...
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Not building database; man-db/auto-update is not 'true'.
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Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-rsem-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-6+rpi1 gcc-8_8.3.0-6+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bowtie_1.0.0-5 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.1 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-6+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.1.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-6+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-6+rpi1 gcc-8-base_8.3.0-6+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 help2man_1.47.8 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-6+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblkid1_2.33.1-0.1 libboost-dev_1.67.0.1+b1 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9.1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcurl3-gnutls_7.64.0-4 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdeflate0_1.2-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.6-2 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.2-1 libgcc-8-dev_8.3.0-6+rpi1 libgcc1_1:8.3.0-6+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.58.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_8.3.0-6+rpi1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-3 libhogweed4_3.4.1-1 libhts-dev_1.9-11 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.0.5-1 libisl19_0.20-2 libk5crypto3_1.17-3 libkeyutils1_1.6-6 libkrb5-3_1.17-3 libkrb5support0_1.17-3 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.1+20181013-2 libncurses5-dev_6.1+20181013-2 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.37.0-1 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.16-1 libpython2-stdlib_2.7.16-1 libpython2.7-minimal_2.7.16-2 libpython2.7-stdlib_2.7.16-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 libsystemd0_241-5+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.3.0-6+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17 mime-support_3.62 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 po-debconf_1.0.21 python_2.7.16-1 python-minimal_2.7.16-1 python2_2.7.16-1 python2-minimal_2.7.16-1 python2.7_2.7.16-2 python2.7-minimal_2.7.16-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rsem-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 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 Jul 12 20:02:47 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./rsem_1.3.2+dfsg-1.dsc
dpkg-source: info: extracting rsem in /<<BUILDDIR>>/rsem-1.3.2+dfsg
dpkg-source: info: unpacking rsem_1.3.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking rsem_1.3.2+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-bc5b264c-c81b-417f-b9ab-3f003d1efd22
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package rsem
dpkg-buildpackage: info: source version 1.3.2+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.3.2+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-1.3.2+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-1.3.2+dfsg/EBSeq'
cd pRSEM && make clean
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.3.2+dfsg/pRSEM'
rm -fr bigWigSummary RLib filterSam2Bed *.pyc
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.2+dfsg/pRSEM'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.2+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-1.3.2+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-1.3.2+dfsg'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.2+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-1.3.2+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-1.3.2+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-1.3.2+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-1.3.2+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-1.3.2+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,
from parseIt.cpp:27:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from utils.h:12,
from parseIt.cpp:13:
/usr/include/c++/8/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++/8/bits/vector.tcc:418:5: 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++/8/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++/8/bits/vector.tcc:418:5: 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++/8/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++/8/bits/vector.tcc:418:5: 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++/8/vector:64,
from utils.h:12,
from parseIt.cpp:13:
/usr/include/c++/8/bits/stl_vector.h: In function 'void parseIt(SamParser*) [with ReadType = PairedEndRead; HitType = PairedEndHit]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h: In function 'void parseIt(SamParser*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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-1.3.2+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
/usr/include/c++/8/bits/stl_vector.h: In function 'void parseIt(SamParser*) [with ReadType = SingleRead; HitType = SingleHit]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h: In function 'void parseIt(SamParser*) [with ReadType = SingleReadQ; HitType = SingleHit]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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-1.3.2+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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.2+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,
from tbam2gbam.cpp:8:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
In file included from tbam2gbam.cpp:8:
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);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from BamWriter.h:14,
from EM.cpp:45:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.2+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 EM.cpp:45:
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);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
EM.cpp: In function 'int main(int, char**)':
EM.cpp:635:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command);
~~~~~~^~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.2+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 wiggle.cpp:8:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.2+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-1.3.2+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:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (b->m_data < b->l_data) {
~~~~~~~~~~^~~~~~~~~~~
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-1.3.2+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
In file included from samValidator.cpp:11:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-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 of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare]
for (int i = 0; i < b->core.n_cigar; ++i) {
~~^~~~~~~~~~~~~~~~~
samValidator.cpp:45:39: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare]
isValid = tb->core.pos >= 0 && tb->core.pos + abs(tb->core.isize) <= header->target_len[tb->core.tid];
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.2+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 scanForPairedEndReads.cpp:11:
sam_utils.h: In function 'void expand_data_size(bam1_t*)':
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-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-1.3.2+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
In file included from /usr/include/c++/8/vector:69,
from EM.cpp:8:
/usr/include/c++/8/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++/8/bits/vector.tcc:478:5: 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++/8/vector:64,
from EM.cpp:8:
/usr/include/c++/8/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++/8/bits/stl_vector.h:867:4: 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++/8/bits/stl_vector.h: In function 'void* E_STEP(void*) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]':
/usr/include/c++/8/bits/stl_vector.h:867:4: 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);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.2+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
/usr/include/c++/8/bits/stl_vector.h: In function 'void* E_STEP(void*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]':
/usr/include/c++/8/bits/stl_vector.h:867:4: 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++/8/bits/stl_vector.h: In function 'void* E_STEP(void*) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]':
/usr/include/c++/8/bits/stl_vector.h:867:4: 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++/8/bits/stl_vector.h: In function 'void* E_STEP(void*) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]':
/usr/include/c++/8/bits/stl_vector.h:867:4: 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);
^~~~~~~~~~~~~~
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++/8/vector:69,
from EM.cpp:8:
/usr/include/c++/8/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++/8/bits/vector.tcc:418:5: 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++/8/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++/8/bits/vector.tcc:418:5: 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++/8/vector:64,
from EM.cpp:8:
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool HitContainer<HitType>::read(std::istream&) [with HitType = SingleHit]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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);
^~~~~~~~~~~~~~~~~
EM.cpp: In function 'void init(ReadReader<ReadType>**&, HitContainer<HitType>**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]':
EM.cpp:127:16: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(datF, "%s.dat", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from EM.cpp:8:
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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);
^~~~~~~~~~~~~~~~~
EM.cpp: In function 'void init(ReadReader<ReadType>**&, HitContainer<HitType>**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]':
EM.cpp:127:16: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(datF, "%s.dat", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from EM.cpp:8:
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/vector:69,
from EM.cpp:8:
/usr/include/c++/8/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++/8/bits/vector.tcc:418:5: 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++/8/vector:64,
from EM.cpp:8:
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool HitContainer<HitType>::read(std::istream&) [with HitType = PairedEndHit]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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);
^~~~~~~~~~~~~~~~~
EM.cpp: In function 'void init(ReadReader<ReadType>**&, HitContainer<HitType>**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]':
EM.cpp:127:16: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(datF, "%s.dat", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from EM.cpp:8:
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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);
^~~~~~~~~~~~~~~~~
EM.cpp: In function 'void init(ReadReader<ReadType>**&, HitContainer<HitType>**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]':
EM.cpp:127:16: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(datF, "%s.dat", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from EM.cpp:8:
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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);
^~~~~~~~~~~~~~~~~
EM.cpp: In function 'void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]':
EM.cpp:435:28: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(out_for_gibbs_F, "%s.ofg", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:484:18: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(thetaF, "%s.theta", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:282:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(modelF, "%s.model", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:505:20: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(outBamF, "%s.transcript.bam", outName);
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp: In function 'void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]':
EM.cpp:435:28: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(out_for_gibbs_F, "%s.ofg", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:484:18: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(thetaF, "%s.theta", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:282:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(modelF, "%s.model", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:505:20: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(outBamF, "%s.transcript.bam", outName);
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp: In function 'void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]':
EM.cpp:435:28: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(out_for_gibbs_F, "%s.ofg", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:484:18: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(thetaF, "%s.theta", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:282:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(modelF, "%s.model", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:505:20: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(outBamF, "%s.transcript.bam", outName);
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp: In function 'void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]':
EM.cpp:435:28: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(out_for_gibbs_F, "%s.ofg", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:484:18: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(thetaF, "%s.theta", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:282:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(modelF, "%s.model", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:505:20: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(outBamF, "%s.transcript.bam", outName);
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp: In function 'int main(int, char**)':
EM.cpp:600:16: warning: '.seq' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(refF, "%s.seq", refName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:604:15: warning: '.ti' directive writing 3 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(tiF, "%s.ti", refName);
^~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 10008 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:607:16: warning: '.cnt' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(cntF, "%s.cnt", statName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:647:21: warning: '.mparams' directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(mparamsF, "%s.mparams", imdName);
^~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 10013 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:619:19: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(thetaF, "%s.theta", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:622:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(modelF, "%s.model", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:631:21: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(outBamF, "%s.transcript.bam", outName);
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EM.cpp:633:21: warning: '%s' directive writing up to 10004 bytes into a region of size 1002 [-Wformat-overflow=]
sprintf(command, "cp %s %s", inpSamF, outBamF);
^~~~~~~~~~ ~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 20013 bytes into a destination of size 1005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Gibbs.cpp: In function 'void init()':
Gibbs.cpp:214:16: warning: '.countvectors' directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(cvsF, "%s.countvectors", imdName);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 14 and 10018 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Gibbs.cpp:225:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(outF, "%s%d", cvsF, i);
^~~~~~
Gibbs.cpp:225:17: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from Gibbs.cpp:7:
/usr/include/c++/8/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++/8/bits/vector.tcc:418:5: 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++/8/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++/8/bits/vector.tcc:418:5: 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++/8/vector:64,
from Gibbs.cpp:7:
/usr/include/c++/8/bits/stl_vector.h: In function 'void load_data(char*, char*, char*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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);
^~~~~~~~~~~~~~~~~
Gibbs.cpp: In function 'int main(int, char**)':
Gibbs.cpp:107:16: warning: '.seq' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(refF, "%s.seq", refName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Gibbs.cpp:112:16: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(ofgF, "%s.ofg", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Gibbs.cpp:495:18: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(modelF, "%s.model", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from Gibbs.cpp:7:
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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);
^~~~~~~~~~~~~~~~~
calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]':
calcCI.cpp:183:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(inpF, "%s%d", cvsF, i);
^~~~~~
calcCI.cpp:183:17: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]':
calcCI.cpp:183:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(inpF, "%s%d", cvsF, i);
^~~~~~
calcCI.cpp:183:17: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]':
calcCI.cpp:183:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(inpF, "%s%d", cvsF, i);
^~~~~~
calcCI.cpp:183:17: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]':
calcCI.cpp:183:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(inpF, "%s%d", cvsF, i);
^~~~~~
calcCI.cpp:183:17: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
calcCI.cpp: In function 'int main(int, char**)':
calcCI.cpp:542:16: warning: '.seq' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(refF, "%s.seq", refName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
calcCI.cpp:546:18: warning: '.grp' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(groupF, "%s.grp", refName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
calcCI.cpp:558:16: warning: '.tmp' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(tmpF, "%s.tmp", imdName);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
calcCI.cpp:559:16: warning: '.countvectors' directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(cvsF, "%s.countvectors", imdName);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 14 and 10018 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
calcCI.cpp:561:18: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=]
sprintf(modelF, "%s.model", statName);
^~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-1.3.2+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="1.3.2+dfsg" \
--name 'Convert GFF3 files to GTF files.' > \
debian/rsem-gff3-to-gtf.1
help2man ./rsem-bam2wig --no-info --version-string="1.3.2+dfsg" \
--name 'Convert BAM files to wiggle files.' > \
debian/rsem-bam2wig.1
help2man ./rsem-simulate-reads --no-info --version-string="1.3.2+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-1.3.2+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-1.3.2+dfsg'
dh_auto_install -- BOOST=/usr/include prefix="/usr"
make -j4 install DESTDIR=/<<BUILDDIR>>/rsem-1.3.2\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.3.2+dfsg'
install --strip-program=true -p rsem-extract-reference-transcripts /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /<<BUILDDIR>>/rsem-1.3.2+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-1.3.2+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /<<BUILDDIR>>/rsem-1.3.2+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /<<BUILDDIR>>/rsem-1.3.2+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-1.3.2+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-1.3.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.2+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.3.2+dfsg'
dh_install
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.2+dfsg'
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_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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-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-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-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-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-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-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-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-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-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-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-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-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: package could avoid a useless dependency if debian/rsem/usr/bin/rsem-build-read-index debian/rsem/usr/bin/rsem-get-unique debian/rsem/usr/bin/rsem-sam-validator debian/rsem/usr/bin/rsem-extract-reference-transcripts debian/rsem/usr/bin/rsem-run-gibbs debian/rsem/usr/bin/rsem-preref debian/rsem/usr/bin/rsem-parse-alignments debian/rsem/usr/bin/rsem-bam2wig debian/rsem/usr/bin/rsem-synthesis-reference-transcripts debian/rsem/usr/bin/rsem-simulate-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-calculate-credibility-intervals debian/rsem/usr/bin/rsem-scan-for-paired-end-reads 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-get-unique debian/rsem/usr/bin/rsem-sam-validator debian/rsem/usr/bin/rsem-parse-alignments debian/rsem/usr/bin/rsem-bam2wig debian/rsem/usr/bin/rsem-run-em debian/rsem/usr/bin/rsem-bam2readdepth debian/rsem/usr/bin/rsem-tbam2gbam debian/rsem/usr/bin/rsem-scan-for-paired-end-reads 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' in '../rsem_1.3.2+dfsg-1_armhf.deb'.
dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.2+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../rsem_1.3.2+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-07-15T13:06:34Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
rsem_1.3.2+dfsg-1_armhf.changes:
--------------------------------
Format: 1.8
Date: Fri, 12 Jul 2019 21:52:15 +0200
Source: rsem
Binary: rsem rsem-dbgsym
Architecture: armhf
Version: 1.3.2+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
rsem - RNA-Seq by Expectation-Maximization
Changes:
rsem (1.3.2+dfsg-1) unstable; urgency=medium
.
* New upstream version
* debhelper 12
* Standards-Version: 4.4.0
* Remove trailing whitespace in debian/changelog
Checksums-Sha1:
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72f9ea28a9a9b9174ae526639ac15e52fbe3c46a 36014436 rsem_1.3.2+dfsg-1_armhf.deb
Checksums-Sha256:
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0044f0437d2db86f6c105813dd5b1d911296f95ce3fabe354a11c9fca84f291c 5849 rsem_1.3.2+dfsg-1_armhf.buildinfo
94e94ac9e978555e600f7ed8de2ba74df5a932ae00927447ae925c47254ac585 36014436 rsem_1.3.2+dfsg-1_armhf.deb
Files:
95ec92f9e96713ac882b279e69302423 5300168 debug optional rsem-dbgsym_1.3.2+dfsg-1_armhf.deb
e54e2014aae7f8bee20d054c122f8390 5849 science optional rsem_1.3.2+dfsg-1_armhf.buildinfo
12b5c502b77517ac19ac3db939bedda7 36014436 science optional rsem_1.3.2+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
rsem-dbgsym_1.3.2+dfsg-1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 5300168 bytes: control archive=1284 bytes.
943 bytes, 12 lines control
1674 bytes, 16 lines md5sums
Package: rsem-dbgsym
Source: rsem
Version: 1.3.2+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5622
Depends: rsem (= 1.3.2+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for rsem
Build-Ids: 017ae488427d34520e0fc1b496283b2e9bb8dce4 1870fa827c18e2cbc2377b5a15bf5fe1f794ba6b 2291265f2677e5753db09654cbcae100f23fb976 22a758df197b381c3edd8a84d5af29c08e87ff27 2517609e44c905c1b5381cd6f0724d7f7eced07c 28c40525f11ea24e9005c76ec1aa44573f508b12 68c0a8b1ee70f0af93722b116a28f8e51d53f778 6aa30503260b9288ac5c859a54ce6823654f002b 732c5b8b96af3638628af71a1d2a7f0fe9143e81 7fcef24a59c7680f2563f72012c9a04877dc1e5a 84d3c3c1553c4217151bc5a22c0befff185e63b4 88ffeac09d2f253462563adcc71f8a046a9912f3 8a5433407488505f56f5c0a10eeae082f7f97219 a51ca76fa542449a1fd2a53b2050e13467424c78 b5c82fa8bf94741218cdad12c09865d1a15315be
drwxr-xr-x root/root 0 2019-07-12 19:52 ./
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 575540 2019-07-12 19:52 ./usr/lib/debug/.build-id/01/7ae488427d34520e0fc1b496283b2e9bb8dce4.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/18/
-rw-r--r-- root/root 336524 2019-07-12 19:52 ./usr/lib/debug/.build-id/18/70fa827c18e2cbc2377b5a15bf5fe1f794ba6b.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root 190432 2019-07-12 19:52 ./usr/lib/debug/.build-id/22/91265f2677e5753db09654cbcae100f23fb976.debug
-rw-r--r-- root/root 209380 2019-07-12 19:52 ./usr/lib/debug/.build-id/22/a758df197b381c3edd8a84d5af29c08e87ff27.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/25/
-rw-r--r-- root/root 486024 2019-07-12 19:52 ./usr/lib/debug/.build-id/25/17609e44c905c1b5381cd6f0724d7f7eced07c.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/28/
-rw-r--r-- root/root 613692 2019-07-12 19:52 ./usr/lib/debug/.build-id/28/c40525f11ea24e9005c76ec1aa44573f508b12.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/68/
-rw-r--r-- root/root 615472 2019-07-12 19:52 ./usr/lib/debug/.build-id/68/c0a8b1ee70f0af93722b116a28f8e51d53f778.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/6a/
-rw-r--r-- root/root 400948 2019-07-12 19:52 ./usr/lib/debug/.build-id/6a/a30503260b9288ac5c859a54ce6823654f002b.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/73/
-rw-r--r-- root/root 383836 2019-07-12 19:52 ./usr/lib/debug/.build-id/73/2c5b8b96af3638628af71a1d2a7f0fe9143e81.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/7f/
-rw-r--r-- root/root 197044 2019-07-12 19:52 ./usr/lib/debug/.build-id/7f/cef24a59c7680f2563f72012c9a04877dc1e5a.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/84/
-rw-r--r-- root/root 191416 2019-07-12 19:52 ./usr/lib/debug/.build-id/84/d3c3c1553c4217151bc5a22c0befff185e63b4.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/88/
-rw-r--r-- root/root 185612 2019-07-12 19:52 ./usr/lib/debug/.build-id/88/ffeac09d2f253462563adcc71f8a046a9912f3.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/8a/
-rw-r--r-- root/root 36612 2019-07-12 19:52 ./usr/lib/debug/.build-id/8a/5433407488505f56f5c0a10eeae082f7f97219.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/a5/
-rw-r--r-- root/root 137540 2019-07-12 19:52 ./usr/lib/debug/.build-id/a5/1ca76fa542449a1fd2a53b2050e13467424c78.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.build-id/b5/
-rw-r--r-- root/root 942600 2019-07-12 19:52 ./usr/lib/debug/.build-id/b5/c82fa8bf94741218cdad12c09865d1a15315be.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 220432 2019-07-12 19:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/rsem.debug
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-07-12 19:52 ./usr/share/doc/rsem-dbgsym -> rsem
rsem_1.3.2+dfsg-1_armhf.deb
---------------------------
new Debian package, version 2.0.
size 36014436 bytes: control archive=2552 bytes.
1557 bytes, 27 lines control
3346 bytes, 48 lines md5sums
Package: rsem
Version: 1.3.2+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 36522
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 2019-07-12 19:52 ./
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/bin/
-rwxr-xr-x root/root 2898 2019-07-12 19:52 ./usr/bin/convert-sam-for-rsem
-rwxr-xr-x root/root 787 2019-07-12 19:52 ./usr/bin/extract-transcript-to-gene-map-from-trinity
-rwxr-xr-x root/root 42640 2019-07-12 19:52 ./usr/bin/rsem-bam2readdepth
-rwxr-xr-x root/root 42640 2019-07-12 19:52 ./usr/bin/rsem-bam2wig
-rwxr-xr-x root/root 13964 2019-07-12 19:52 ./usr/bin/rsem-build-read-index
-rwxr-xr-x root/root 214680 2019-07-12 19:52 ./usr/bin/rsem-calculate-credibility-intervals
-rwxr-xr-x root/root 72989 2019-07-12 19:52 ./usr/bin/rsem-calculate-expression
-rwxr-xr-x root/root 3312 2019-07-12 19:52 ./usr/bin/rsem-control-fdr
-rwxr-xr-x root/root 71308 2019-07-12 19:52 ./usr/bin/rsem-extract-reference-transcripts
-rwxr-xr-x root/root 5605 2019-04-06 21:04 ./usr/bin/rsem-gen-transcript-plots
-rwxr-xr-x root/root 1975 2019-07-12 19:52 ./usr/bin/rsem-generate-data-matrix
-rwxr-xr-x root/root 3470 2019-07-12 19:52 ./usr/bin/rsem-generate-ngvector
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-rwxr-xr-x root/root 495 2019-04-06 21:04 ./usr/bin/rsem-refseq-extract-primary-assembly
-rwxr-xr-x root/root 300700 2019-07-12 19:52 ./usr/bin/rsem-run-em
-rwxr-xr-x root/root 202392 2019-07-12 19:52 ./usr/bin/rsem-run-gibbs
-rwxr-xr-x root/root 38544 2019-07-12 19:52 ./usr/bin/rsem-sam-validator
-rwxr-xr-x root/root 42640 2019-07-12 19:52 ./usr/bin/rsem-scan-for-paired-end-reads
-rwxr-xr-x root/root 194200 2019-07-12 19:52 ./usr/bin/rsem-simulate-reads
-rwxr-xr-x root/root 71308 2019-07-12 19:52 ./usr/bin/rsem-synthesis-reference-transcripts
-rwxr-xr-x root/root 87696 2019-07-12 19:52 ./usr/bin/rsem-tbam2gbam
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drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/doc/rsem/
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-rw-r--r-- root/root 431 2019-07-12 19:52 ./usr/share/doc/rsem/README.test
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-rw-r--r-- root/root 1169 2019-07-12 19:52 ./usr/share/doc/rsem/copyright
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/doc/rsem/examples/
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-rw-r--r-- root/root 415 2019-07-12 19:52 ./usr/share/doc/rsem/run-unit-test
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/man/
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/man/man1/
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-rw-r--r-- root/root 13731 2019-07-12 19:52 ./usr/share/man/man1/rsem-calculate-expression.1.gz
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-rw-r--r-- root/root 3251 2019-07-12 19:52 ./usr/share/man/man1/rsem-plot-transcript-wiggles.1.gz
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-rw-r--r-- root/root 3668 2019-07-12 19:52 ./usr/share/man/man1/rsem-run-ebseq.1.gz
-rw-r--r-- root/root 1804 2019-07-12 19:52 ./usr/share/man/man1/rsem-simulate-reads.1.gz
drwxr-xr-x root/root 0 2019-07-12 19:52 ./usr/share/perl5/
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+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 170168
Build-Time: 429
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 591
Job: rsem_1.3.2+dfsg-1
Machine Architecture: armhf
Package: rsem
Package-Time: 1107
Source-Version: 1.3.2+dfsg-1
Space: 170168
Status: successful
Version: 1.3.2+dfsg-1
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Finished at 2019-07-15T13:06:34Z
Build needed 00:18:27, 170168k disc space