rsem →
1.3.1+dfsg-1 →
armhf → 2018-09-29 04:52:31
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| rsem 1.3.1+dfsg-1 (armhf) Sat, 29 Sep 2018 04:46:02 +0000 |
+==============================================================================+
Package: rsem
Version: 1.3.1+dfsg-1
Source Version: 1.3.1+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-c4c45c5d-4c91-40d0-bee6-fae1a545ec71' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 MB]
Fetched 23.9 MB in 12s (2074 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'rsem' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/rsem.git
Please use:
git clone https://salsa.debian.org/med-team/rsem.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 35.9 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main rsem 1.3.1+dfsg-1 (dsc) [2104 B]
Get:2 http://172.17.0.1/private buster-staging/main rsem 1.3.1+dfsg-1 (tar) [274 kB]
Get:3 http://172.17.0.1/private buster-staging/main rsem 1.3.1+dfsg-1 (diff) [35.7 MB]
Fetched 35.9 MB in 12s (2933 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/rsem-5iVyuG/rsem-1.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/rsem-5iVyuG' 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-KX2rK5/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-KX2rK5/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-KX2rK5/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-KX2rK5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (11.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 74 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-KX2rK5/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 ... 15689 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), zlib1g-dev, libncurses5-dev, libboost-dev, perl, python, help2man, libhts-dev, bowtie | bowtie2
Filtered Build-Depends: debhelper (>= 11~), zlib1g-dev, libncurses5-dev, libboost-dev, perl, python, help2man, libhts-dev, bowtie
dpkg-deb: building package 'sbuild-build-depends-rsem-dummy' in '/<<BUILDDIR>>/resolver-KX2rK5/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-KX2rK5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ Sources [537 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ Packages [614 B]
Fetched 2484 B in 0s (12.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install rsem build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bowtie bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libboost-dev
libboost1.62-dev libbsd0 libcroco3 libcurl3-gnutls libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libhts-dev libhts2 libicu-le-hb0 libicu60
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev
libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib
libpython2.7-minimal libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1
libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python
python-minimal python2 python2-minimal python2.7 python2.7-minimal
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc bowtie-examples wamerican
| wordlist whois vacation dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff libboost-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user
liblzma-doc ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk
python2-doc python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bowtie bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libboost-dev
libboost1.62-dev libbsd0 libcroco3 libcurl3-gnutls libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libhts-dev libhts2 libicu-le-hb0 libicu60
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev
libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib
libpython2.7-minimal libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1
libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python
python-minimal python2 python2-minimal python2.7 python2.7-minimal
sbuild-build-depends-rsem-dummy zlib1g-dev
0 upgraded, 68 newly installed, 0 to remove and 74 not upgraded.
Need to get 32.7 MB/34.1 MB of archives.
After this operation, 210 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KX2rK5/apt_archive ./ sbuild-build-depends-rsem-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b2 [18.3 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-4 [394 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-4 [1088 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-4 [1843 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-4 [299 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.3 [12.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-4 [547 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.8-2+rpi1 [860 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.7 [176 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-10 [7003 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:51 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-1 [52.5 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.61.0-1 [281 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180714-1 [279 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180714-1 [940 B]
Get:60 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf bowtie armhf 1.0.0-5 [1320 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up bsdmainutils (11.1.2) ...
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Processing triggers for libc-bin (2.27-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.1.0-12+rpi1 gcc-8_8.1.0-12+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bowtie_1.0.0-5 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.1.0-12+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.1.0-12+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.1.0-12+rpi1 gcc-8-base_8.1.0-12+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gnupg_2.2.9-1+rpi1 gnupg-agent_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 help2man_1.47.7 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.1.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.1.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libblkid1_2.32.1-0.1 libboost-dev_1.62.0.1+b8 libboost1.62-dev_1.62.0+dfsg-10 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-12+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.61.0-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.1.0-12+rpi1 libgcc1_1:8.1.0-12+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.1.0-12+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libgssapi-krb5-2_1.16-2 libharfbuzz0b_1.8.8-2+rpi1 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180714-1 libncurses5_6.1+20180714-1 libncurses5-dev_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.6-1 libnss-systemd_239-7 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-10 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-1 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-4 libpython2.7-stdlib_2.7.15-4 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssh2-1_1.8.0-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 libsystemd0_239-7 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-4 libubsan1_8.1.0-12+rpi1 libudev1_239-7 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-4 python2.7-minimal_2.7.15-4 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_4.5-1 sensible-utils_0.0.12 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Sep 26 19:44:35 2018 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_1.3.1+dfsg-1.dsc
dpkg-source: info: extracting rsem in /<<BUILDDIR>>/rsem-1.3.1+dfsg
dpkg-source: info: unpacking rsem_1.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking rsem_1.3.1+dfsg-1.debian.tar.xz
dpkg-source: info: applying hardening
dpkg-source: info: applying use_debian_packaged_samtools.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-c4c45c5d-4c91-40d0-bee6-fae1a545ec71
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package rsem
dpkg-buildpackage: info: source version 1.3.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build rsem-1.3.1+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.3.1+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-1.3.1+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-1.3.1+dfsg/EBSeq'
cd pRSEM && make clean
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.3.1+dfsg/pRSEM'
rm -fr bigWigSummary RLib filterSam2Bed *.pyc
make[2]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.1+dfsg/pRSEM'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.1+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-1.3.1+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-1.3.1+dfsg'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.1+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-1.3.1+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-1.3.1+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-1.3.1+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-1.3.1+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-1.3.1+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);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.1+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 = 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-1.3.1+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
/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-1.3.1+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);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp
In file included from BamWriter.h:14,
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-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp
In file included from EM.cpp:45:
BamWriter.h: In constructor 'BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)':
BamWriter.h:70:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(out, out_header);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
BamWriter.h: In member function 'void BamWriter::work(HitWrapper<SingleHit>)':
BamWriter.h:101:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, b);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BamWriter.h: In member function 'void BamWriter::work(HitWrapper<PairedEndHit>)':
BamWriter.h:136:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, b);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BamWriter.h:137:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(out, out_header, b2);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from wiggle.cpp:8:
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-1.3.1+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-1.3.1+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-1.3.1+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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp
In file included from samValidator.cpp:11:
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];
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp
g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o
g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o
g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o
g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o
g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz
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);
^~~~~~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz
/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);
^~~~~~~~~~~~~~
/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);
^~~~~~~~~~~~~~
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 = 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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 = 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:624:20: 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:862,
from /usr/include/c++/8/cstdio:42,
from EM.cpp:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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 ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:862,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from Gibbs.cpp:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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:862,
from /usr/include/c++/8/cstdio:42,
from calcCI.cpp:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: 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-1.3.1+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="1.3.1+dfsg" \
--name 'Convert GFF3 files to GTF files.' > \
debian/rsem-gff3-to-gtf.1
help2man ./rsem-bam2wig --no-info --version-string="1.3.1+dfsg" \
--name 'Convert BAM files to wiggle files.' > \
debian/rsem-bam2wig.1
help2man ./rsem-simulate-reads --no-info --version-string="1.3.1+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-1.3.1+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-1.3.1+dfsg'
dh_auto_install -- BOOST=/usr/include prefix="/usr"
make -j4 install DESTDIR=/<<BUILDDIR>>/rsem-1.3.1\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr
make[2]: Entering directory '/<<BUILDDIR>>/rsem-1.3.1+dfsg'
install --strip-program=true -p rsem-extract-reference-transcripts /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /<<BUILDDIR>>/rsem-1.3.1+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-1.3.1+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /<<BUILDDIR>>/rsem-1.3.1+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /<<BUILDDIR>>/rsem-1.3.1+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-1.3.1+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-1.3.1+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/rsem-1.3.1+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/rsem-1.3.1+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-1.3.1+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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-simulate-reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-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-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-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-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-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-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-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-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-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-scan-for-paired-end-reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/rsem/usr/bin/rsem-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-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-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-preref 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-sam-validator debian/rsem/usr/bin/rsem-run-em debian/rsem/usr/bin/rsem-get-unique debian/rsem/usr/bin/rsem-parse-alignments debian/rsem/usr/bin/rsem-bam2readdepth debian/rsem/usr/bin/rsem-scan-for-paired-end-reads debian/rsem/usr/bin/rsem-bam2wig debian/rsem/usr/bin/rsem-tbam2gbam were not linked against libz.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/rsem/usr/bin/rsem-simulate-reads debian/rsem/usr/bin/rsem-sam-validator debian/rsem/usr/bin/rsem-run-gibbs debian/rsem/usr/bin/rsem-run-em debian/rsem/usr/bin/rsem-extract-reference-transcripts debian/rsem/usr/bin/rsem-calculate-credibility-intervals debian/rsem/usr/bin/rsem-get-unique debian/rsem/usr/bin/rsem-build-read-index debian/rsem/usr/bin/rsem-parse-alignments debian/rsem/usr/bin/rsem-bam2readdepth debian/rsem/usr/bin/rsem-scan-for-paired-end-reads debian/rsem/usr/bin/rsem-bam2wig debian/rsem/usr/bin/rsem-tbam2gbam debian/rsem/usr/bin/rsem-synthesis-reference-transcripts debian/rsem/usr/bin/rsem-preref were not linked against ld-linux-armhf.so.3 (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_1.3.1+dfsg-1_armhf.deb'.
dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.1+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../rsem_1.3.1+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build rsem-1.3.1+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-09-29T04:52:26Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
rsem_1.3.1+dfsg-1_armhf.changes:
--------------------------------
Format: 1.8
Date: Wed, 26 Sep 2018 21:41:44 +0200
Source: rsem
Binary: rsem
Architecture: armhf
Version: 1.3.1+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
rsem - RNA-Seq by Expectation-Maximization
Changes:
rsem (1.3.1+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Standards-Version: 4.2.1
* Fix Perl interpreter path
* Remove unneeded get-orig-source target
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Checksums-Sha256:
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Files:
adaab14583596a68cd18c8bee5047de6 5631636 debug optional rsem-dbgsym_1.3.1+dfsg-1_armhf.deb
88d768c1f57d4045cee6439826acbed0 6043 science optional rsem_1.3.1+dfsg-1_armhf.buildinfo
fceb9929a14536e4601b622e04429220 36009984 science optional rsem_1.3.1+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
rsem-dbgsym_1.3.1+dfsg-1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 5631636 bytes: control archive=1236 bytes.
943 bytes, 12 lines control
1590 bytes, 15 lines md5sums
Package: rsem-dbgsym
Source: rsem
Version: 1.3.1+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5943
Depends: rsem (= 1.3.1+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for rsem
Build-Ids: 199608704a0271c81baae037222b64448f426693 3bfb456406108797b41532c1d6ee3a3473f6be18 6fc7a6e63f218cd6eed3dacf8b95c25cab07f488 7085b8cad3c0b6fb03a5ef79599c03853737d59d 8ebd7e855ad2807c4f7a394d7f5fce3fa0897a61 924982b8f9a480f1a2d9d538af44164be81a8526 b09cc644d96041d28711d053d415a8940d2d713e b234884101ef25ce4e7bdad0fda44f48c5976373 bfa79af3937a908c44bf92e2b075b46b7e85953f c138e28c3780640df4a8224c7ddc6b62d715e284 c1592b4e9bd71ffa1d6d7d36fb798084ab10361c ea1015026689a5061fc031a2b8da28a1e24b223e eaed27e9a07d0b1d591cfa60c682e887b59ee02c eb40a2c46b1aa16f9d3ecddae18784a1ed4e9167 f2767d0ffbe826034d9dec8a844a986a18e74152
drwxr-xr-x root/root 0 2018-09-26 19:41 ./
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/19/
-rw-r--r-- root/root 1019628 2018-09-26 19:41 ./usr/lib/debug/.build-id/19/9608704a0271c81baae037222b64448f426693.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/3b/
-rw-r--r-- root/root 216432 2018-09-26 19:41 ./usr/lib/debug/.build-id/3b/fb456406108797b41532c1d6ee3a3473f6be18.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/6f/
-rw-r--r-- root/root 669988 2018-09-26 19:41 ./usr/lib/debug/.build-id/6f/c7a6e63f218cd6eed3dacf8b95c25cab07f488.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/70/
-rw-r--r-- root/root 232196 2018-09-26 19:41 ./usr/lib/debug/.build-id/70/85b8cad3c0b6fb03a5ef79599c03853737d59d.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/8e/
-rw-r--r-- root/root 404384 2018-09-26 19:41 ./usr/lib/debug/.build-id/8e/bd7e855ad2807c4f7a394d7f5fce3fa0897a61.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/92/
-rw-r--r-- root/root 665392 2018-09-26 19:41 ./usr/lib/debug/.build-id/92/4982b8f9a480f1a2d9d538af44164be81a8526.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/b0/
-rw-r--r-- root/root 432328 2018-09-26 19:41 ./usr/lib/debug/.build-id/b0/9cc644d96041d28711d053d415a8940d2d713e.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/b2/
-rw-r--r-- root/root 629432 2018-09-26 19:41 ./usr/lib/debug/.build-id/b2/34884101ef25ce4e7bdad0fda44f48c5976373.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 523544 2018-09-26 19:41 ./usr/lib/debug/.build-id/bf/a79af3937a908c44bf92e2b075b46b7e85953f.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/c1/
-rw-r--r-- root/root 209228 2018-09-26 19:41 ./usr/lib/debug/.build-id/c1/38e28c3780640df4a8224c7ddc6b62d715e284.debug
-rw-r--r-- root/root 238792 2018-09-26 19:41 ./usr/lib/debug/.build-id/c1/592b4e9bd71ffa1d6d7d36fb798084ab10361c.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/ea/
-rw-r--r-- root/root 49044 2018-09-26 19:41 ./usr/lib/debug/.build-id/ea/1015026689a5061fc031a2b8da28a1e24b223e.debug
-rw-r--r-- root/root 233224 2018-09-26 19:41 ./usr/lib/debug/.build-id/ea/ed27e9a07d0b1d591cfa60c682e887b59ee02c.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/eb/
-rw-r--r-- root/root 369124 2018-09-26 19:41 ./usr/lib/debug/.build-id/eb/40a2c46b1aa16f9d3ecddae18784a1ed4e9167.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/lib/debug/.build-id/f2/
-rw-r--r-- root/root 163364 2018-09-26 19:41 ./usr/lib/debug/.build-id/f2/767d0ffbe826034d9dec8a844a986a18e74152.debug
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-09-26 19:41 ./usr/share/doc/rsem-dbgsym -> rsem
rsem_1.3.1+dfsg-1_armhf.deb
---------------------------
new Debian package, version 2.0.
size 36009984 bytes: control archive=2552 bytes.
1557 bytes, 27 lines control
3346 bytes, 48 lines md5sums
Package: rsem
Version: 1.3.1+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 36509
Depends: libc6 (>= 2.15), libgcc1 (>= 1:3.5), libhts2 (>= 1.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), perl, r-base-core, bowtie | bowtie2, python
Suggests: r-bioc-ebseq
Section: science
Priority: optional
Homepage: http://deweylab.biostat.wisc.edu/rsem/
Description: RNA-Seq by Expectation-Maximization
RSEM is a software package for estimating gene and isoform expression
levels from RNA-Seq data. The RSEM package provides an user-friendly
interface, supports threads for parallel computation of the EM
algorithm, single-end and paired-end read data, quality scores,
variable-length reads and RSPD estimation. In addition, it provides
posterior mean and 95% credibility interval estimates for expression
levels. For visualization, It can generate BAM and Wiggle files in both
transcript-coordinate and genomic-coordinate. Genomic-coordinate files
can be visualized by both UCSC Genome browser and Broad Institute’s
Integrative Genomics Viewer (IGV). Transcript-coordinate files can be
visualized by IGV. RSEM also has its own scripts to generate transcript
read depth plots in pdf format. The unique feature of RSEM is, the read
depth plots can be stacked, with read depth contributed to unique reads
shown in black and contributed to multi-reads shown in red. In addition,
models learned from data can also be visualized. Last but not least,
RSEM contains a simulator.
drwxr-xr-x root/root 0 2018-09-26 19:41 ./
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/bin/
-rwxr-xr-x root/root 2898 2018-09-26 19:41 ./usr/bin/convert-sam-for-rsem
-rwxr-xr-x root/root 787 2018-09-26 19:41 ./usr/bin/extract-transcript-to-gene-map-from-trinity
-rwxr-xr-x root/root 42508 2018-09-26 19:41 ./usr/bin/rsem-bam2readdepth
-rwxr-xr-x root/root 42508 2018-09-26 19:41 ./usr/bin/rsem-bam2wig
-rwxr-xr-x root/root 13832 2018-09-26 19:41 ./usr/bin/rsem-build-read-index
-rwxr-xr-x root/root 210452 2018-09-26 19:41 ./usr/bin/rsem-calculate-credibility-intervals
-rwxr-xr-x root/root 72635 2018-09-26 19:41 ./usr/bin/rsem-calculate-expression
-rwxr-xr-x root/root 3312 2018-09-26 19:41 ./usr/bin/rsem-control-fdr
-rwxr-xr-x root/root 71176 2018-09-26 19:41 ./usr/bin/rsem-extract-reference-transcripts
-rwxr-xr-x root/root 5605 2018-06-27 18:52 ./usr/bin/rsem-gen-transcript-plots
-rwxr-xr-x root/root 1975 2018-09-26 19:41 ./usr/bin/rsem-generate-data-matrix
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-rwxr-xr-x root/root 194068 2018-09-26 19:41 ./usr/bin/rsem-simulate-reads
-rwxr-xr-x root/root 67080 2018-09-26 19:41 ./usr/bin/rsem-synthesis-reference-transcripts
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drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/doc/rsem/
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-rw-r--r-- root/root 431 2018-09-26 19:41 ./usr/share/doc/rsem/README.test
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-rw-r--r-- root/root 1056 2018-09-26 19:41 ./usr/share/doc/rsem/changelog.Debian.gz
-rw-r--r-- root/root 1398 2018-06-27 18:52 ./usr/share/doc/rsem/cnt_file_description.txt
-rw-r--r-- root/root 1169 2018-09-26 19:41 ./usr/share/doc/rsem/copyright
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/doc/rsem/examples/
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drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/man/
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/man/man1/
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-rw-r--r-- root/root 1804 2018-09-26 19:41 ./usr/share/man/man1/rsem-simulate-reads.1.gz
drwxr-xr-x root/root 0 2018-09-26 19:41 ./usr/share/perl5/
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+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 170720
Build-Time: 109
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 242
Job: rsem_1.3.1+dfsg-1
Machine Architecture: armhf
Package: rsem
Package-Time: 384
Source-Version: 1.3.1+dfsg-1
Space: 170720
Status: successful
Version: 1.3.1+dfsg-1
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Finished at 2018-09-29T04:52:26Z
Build needed 00:06:24, 170720k disk space