tophat →
2.1.1+dfsg1-1 →
armhf → 2017-12-13 07:26:52
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| tophat 2.1.1+dfsg1-1 (armhf) Wed, 13 Dec 2017 07:16:31 +0000 |
+==============================================================================+
Package: tophat
Version: 2.1.1+dfsg1-1
Source Version: 2.1.1+dfsg1-1
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-5711fae3-fd5a-42e9-b86a-3a351bc40db3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.2 MB]
Fetched 22.7 MB in 8s (2774 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: 'tophat' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/tophat.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/tophat.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 371 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main tophat 2.1.1+dfsg1-1 (dsc) [2179 B]
Get:2 http://172.17.0.1/private buster-staging/main tophat 2.1.1+dfsg1-1 (tar) [350 kB]
Get:3 http://172.17.0.1/private buster-staging/main tophat 2.1.1+dfsg1-1 (diff) [18.4 kB]
Fetched 371 kB in 0s (2620 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tophat-VFvtj7/tophat-2.1.1+dfsg1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tophat-VFvtj7' 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-9uJbVN/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-9uJbVN/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-9uJbVN/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-9uJbVN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (6805 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 54 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (38.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15134 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 (>= 10), libbam-dev, zlib1g-dev, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man, bowtie
Filtered Build-Depends: debhelper (>= 10), libbam-dev, zlib1g-dev, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man, bowtie
dpkg-deb: building package 'sbuild-build-depends-tophat-dummy' in '/<<BUILDDIR>>/resolver-9uJbVN/apt_archive/sbuild-build-depends-tophat-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-tophat-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-9uJbVN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ Sources [545 B]
Get:5 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ Packages [623 B]
Fetched 2501 B in 0s (7890 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install tophat 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 e2fsprogs-l10n libsasl2-modules openssl
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 file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbam-dev
libboost-atomic1.62-dev libboost-atomic1.62.0 libboost-chrono1.62-dev
libboost-chrono1.62.0 libboost-date-time1.62-dev libboost-date-time1.62.0
libboost-serialization1.62-dev libboost-serialization1.62.0
libboost-system-dev libboost-system1.62-dev libboost-system1.62.0
libboost-thread-dev libboost-thread1.62-dev libboost-thread1.62.0
libboost1.62-dev libbsd0 libcroco3 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl
libtool libxml2 m4 man-db mime-support po-debconf python python-minimal
python2.7 python2.7-minimal seqan-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc bowtie-examples wamerican
| wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev
libgettextpo-dev groff libboost1.62-doc libboost-context1.62-dev
libboost-coroutine1.62-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-signals1.62-dev
libboost-test1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev
libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
apparmor libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs 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 file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbam-dev
libboost-atomic1.62-dev libboost-atomic1.62.0 libboost-chrono1.62-dev
libboost-chrono1.62.0 libboost-date-time1.62-dev libboost-date-time1.62.0
libboost-serialization1.62-dev libboost-serialization1.62.0
libboost-system-dev libboost-system1.62-dev libboost-system1.62.0
libboost-thread-dev libboost-thread1.62-dev libboost-thread1.62.0
libboost1.62-dev libbsd0 libcroco3 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl
libtool libxml2 m4 man-db mime-support po-debconf python python-minimal
python2.7 python2.7-minimal sbuild-build-depends-tophat-dummy seqan-dev
zlib1g-dev
0 upgraded, 60 newly installed, 0 to remove and 54 not upgraded.
Need to get 33.2 MB of archives.
After this operation, 215 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-9uJbVN/apt_archive ./ sbuild-build-depends-tophat-dummy 0.invalid.0 [912 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 groff-base armhf 1.22.3-9 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-3 [95.9 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 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 2.7.6.1-4 [1012 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-4 [393 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-4 [1075 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.14-1 [40.7 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-2 [73.6 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.14-4 [1841 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.14-4 [293 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.14-1 [20.1 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-1 [155 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5.1 [608 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1+nmu1 [74.2 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 15 [16.2 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.10.9 [975 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.5 [162 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4+b2 [7053 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libboost-atomic1.62.0 armhf 1.62.0+dfsg-4+b2 [31.4 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libboost-atomic1.62-dev armhf 1.62.0+dfsg-4+b2 [29.8 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libboost-system1.62.0 armhf 1.62.0+dfsg-4+b2 [32.4 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libboost-chrono1.62.0 armhf 1.62.0+dfsg-4+b2 [36.0 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libboost-chrono1.62-dev armhf 1.62.0+dfsg-4+b2 [37.6 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libboost-date-time1.62.0 armhf 1.62.0+dfsg-4+b2 [41.5 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.62.0 armhf 1.62.0+dfsg-4+b2 [106 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.62-dev armhf 1.62.0+dfsg-4+b2 [171 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libboost-date-time1.62-dev armhf 1.62.0+dfsg-4+b2 [51.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libboost-system1.62-dev armhf 1.62.0+dfsg-4+b2 [33.4 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libboost-system-dev armhf 1.62.0.1+b8 [3838 B]
Get:55 http://172.17.0.1/private buster-staging/main armhf libboost-thread1.62.0 armhf 1.62.0+dfsg-4+b2 [65.2 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libboost-thread1.62-dev armhf 1.62.0+dfsg-4+b2 [71.5 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libboost-thread-dev armhf 1.62.0.1+b8 [3730 B]
Get:58 http://172.17.0.1/private buster-staging/main armhf seqan-dev all 1.4.2+dfsg-2 [1098 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf bowtie armhf 1.0.0-5 [1320 kB]
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Setting up libexpat1:armhf (2.2.3-2) ...
Setting up bowtie (1.0.0-5) ...
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Setting up mime-support (3.60) ...
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Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.1-1) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.6-3) ...
Setting up libboost-serialization1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-5.1) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Processing triggers for libc-bin (2.25-2+rpi1) ...
Setting up autotools-dev (20161112.1+nmu1) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up libboost-atomic1.62.0:armhf (1.62.0+dfsg-4+b2) ...
Setting up liblocale-gettext-perl (1.07-3+b2) ...
Setting up bsdmainutils (9.0.14) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpython2.7-stdlib:armhf (2.7.14-4) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up libboost-system1.62.0:armhf (1.62.0+dfsg-4+b2) ...
Setting up seqan-dev (1.4.2+dfsg-2) ...
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Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up libboost-atomic1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Setting up libboost-date-time1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Setting up gettext (0.19.8.1-4) ...
Setting up libboost-thread1.62.0:armhf (1.62.0+dfsg-4+b2) ...
Setting up python2.7 (2.7.14-4) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up libpython-stdlib:armhf (2.7.14-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
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Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Setting up libboost-chrono1.62.0:armhf (1.62.0+dfsg-4+b2) ...
Setting up libtool (2.4.6-2) ...
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Setting up libboost-chrono1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Setting up libboost-thread1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Setting up libboost-thread-dev:armhf (1.62.0.1+b8) ...
Setting up dh-autoreconf (15) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (10.10.9) ...
Setting up sbuild-build-depends-tophat-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.25-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-8+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-14 gcc-7_7.2.0-14 libc6-dev_2.25-2+rpi1 libstdc++-7-dev_7.2.0-14 libstdc++6_7.2.0-14 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-8+rpi1 binutils-arm-linux-gnueabihf_2.29.1-8+rpi1 binutils-common_2.29.1-8+rpi1 bowtie_1.0.0-5 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-14 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.9 debianutils_4.8.3 dh-autoreconf_15 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.2-1+rpi1 dmsetup_2:1.02.145-4 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 e2fsprogs-l10n_1.43.7-1 fakeroot_1.22-2 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1d1 g++-7_7.2.0-14 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-14 gcc-7-base_7.2.0-14 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.2-1+rpi1 gnupg-agent_2.2.2-1+rpi1 gnupg-l10n_2.2.2-1+rpi1 gnupg-utils_2.2.2-1+rpi1 gpg_2.2.2-1+rpi1 gpg-agent_2.2.2-1+rpi1 gpg-wks-client_2.2.2-1+rpi1 gpg-wks-server_2.2.2-1+rpi1 gpgconf_2.2.2-1+rpi1 gpgsm_2.2.2-1+rpi1 gpgv_2.2.2-1+rpi1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.5 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.1-3 libapt-pkg5.0_1.6~alpha5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-14 libassuan0_2.4.4-1 libatomic1_7.2.0-14 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-2 libaudit1_1:2.8.1-2 libbam-dev_0.1.19-2 libbinutils_2.29.1-8+rpi1 libblkid1_2.30.2-0.1 libboost-atomic1.62-dev_1.62.0+dfsg-4+b2 libboost-atomic1.62.0_1.62.0+dfsg-4+b2 libboost-chrono1.62-dev_1.62.0+dfsg-4+b2 libboost-chrono1.62.0_1.62.0+dfsg-4+b2 libboost-date-time1.62-dev_1.62.0+dfsg-4+b2 libboost-date-time1.62.0_1.62.0+dfsg-4+b2 libboost-serialization1.62-dev_1.62.0+dfsg-4+b2 libboost-serialization1.62.0_1.62.0+dfsg-4+b2 libboost-system-dev_1.62.0.1+b8 libboost-system1.62-dev_1.62.0+dfsg-4+b2 libboost-system1.62.0_1.62.0+dfsg-4+b2 libboost-thread-dev_1.62.0.1+b8 libboost-thread1.62-dev_1.62.0+dfsg-4+b2 libboost-thread1.62.0_1.62.0+dfsg-4+b2 libboost1.62-dev_1.62.0+dfsg-4+b2 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.25-2+rpi1 libc-dev-bin_2.25-2+rpi1 libc6_2.25-2+rpi1 libc6-dev_2.25-2+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-14 libcilkrts5_7.2.0-14 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.2-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.145-4 libdpkg-perl_1.19.0.4 libdrm-common_2.4.88-1+rpi1 libdrm2_2.4.88-1+rpi1 libexpat1_2.2.3-2 libfakeroot_1.22-2 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-14 libgcc1_1:7.2.0-14 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-14 libgpg-error0_1.27-5 libhogweed4_3.3-2 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.1-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpython-stdlib_2.7.14-1 libpython2.7-minimal_2.7.14-4 libpython2.7-stdlib_2.7.14-4 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.21.0-1 libss2_1.43.7-1 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-14 libstdc++6_7.2.0-14 libsystemd0_235-3 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-14 libudev1_235-3 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5.1 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-4 mawk_1.3.3-17 mime-support_3.60 mount_2.30.2-0.1 multiarch-support_2.25-2+rpi1 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0g-2 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.14-1 python-minimal_2.7.14-1 python2.7_2.7.14-4 python2.7-minimal_2.7.14-4 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tophat-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 seqan-dev_1.4.2+dfsg-2 systemd_235-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017c-1 udev_235-3 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Dec 7 17:00:00 2017 UTC
gpgv: using RSA key 8B7868786C33E5C64C4D0A480816B9E18C762BAD
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./tophat_2.1.1+dfsg1-1.dsc
dpkg-source: info: extracting tophat in /<<BUILDDIR>>/tophat-2.1.1+dfsg1
dpkg-source: info: unpacking tophat_2.1.1+dfsg1.orig.tar.xz
dpkg-source: info: unpacking tophat_2.1.1+dfsg1-1.debian.tar.xz
dpkg-source: info: applying remove_3rd_party_code.patch
dpkg-source: info: applying fix_includes_path.patch
dpkg-source: info: applying fix-gcc6.patch
dpkg-source: info: applying remove-convenience-copy-of-samtools.patch
dpkg-source: info: applying fix-compatibility-with-recent-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-5711fae3-fd5a-42e9-b86a-3a351bc40db3
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package tophat
dpkg-buildpackage: info: source version 2.1.1+dfsg1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build tophat-2.1.1+dfsg1
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --no-parallel
dh_clean -O--no-parallel
debian/rules build-arch
dh build-arch --no-parallel
dh_update_autotools_config -a -O--no-parallel
dh_autoreconf -a -O--no-parallel
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
configure.ac:20: installing './compile'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_auto_configure -- --with-boost-libdir=/usr/lib/arm-linux-gnueabihf
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --with-boost-libdir=/usr/lib/arm-linux-gnueabihf
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gawk... (cached) mawk
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) none
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/dist-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages
checking for boostlib >= 1.38.0... yes
checking whether the compiler implements namespaces... yes
checking whether the Boost::Thread library is available... yes
checking for main in -lboost_thread... yes
checking whether Boost::Thread needs Boost::System library... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for ANSI C header files... (cached) yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking for an ANSI C-conforming const... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for gzread in -lz... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for memset... yes
checking for strdup... yes
checking for strrchr... yes
checking for strtol... yes
checking for strsep... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) none
checking dependency style of g++... (cached) none
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
-- tophat 2.1.1 Configuration Results --
C++ compiler: g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include
Linker flags: -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now
BOOST libraries: -lboost_thread -lboost_system
GCC version: gcc (Raspbian 7.2.0-14) 7.2.0
Host System type: arm-unknown-linux-gnueabihf
Install prefix: /usr
Install eprefix: ${prefix}
See config.h for further configuration information.
Email bug reports to <tophat.cufflinks@gmail.com>.
make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_auto_build -a -O--no-parallel
make -j1
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
Making all in src
make[3]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GBase.o GBase.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o codons.o codons.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gdna.o gdna.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GStr.o GStr.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GFaSeqGet.o GFaSeqGet.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gff.o gff.cpp
rm -f libgc.a
ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgc.a
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o reads.o reads.cpp
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alphabet.o alphabet.c
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bwt_map.o bwt_map.cpp
bwt_map.cpp: In function 'bool spliceCigar(std::vector<CigarOp>&, const std::vector<CigarOp>&, std::vector<bool>, int&, int, int, CigarOpCode, int&)':
bwt_map.cpp:705:9: warning: variable 'prev_opcode' set but not used [-Wunused-but-set-variable]
int prev_opcode=0;
^~~~~~~~~~~
bwt_map.cpp:706:9: warning: variable 'prev_oplen' set but not used [-Wunused-but-set-variable]
int prev_oplen=0;
^~~~~~~~~~
bwt_map.cpp: In member function 'virtual bool BAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)':
bwt_map.cpp:1112:7: warning: variable 'text_mate_pos' set but not used [-Wunused-but-set-variable]
int text_mate_pos = hit_buf->core.mpos;
^~~~~~~~~~~~~
bwt_map.cpp:1118:7: warning: variable 'num_hits' set but not used [-Wunused-but-set-variable]
int num_hits = 1;
^~~~~~~~
bwt_map.cpp: In member function 'virtual bool SplicedBAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)':
bwt_map.cpp:1481:7: warning: variable 'text_mate_pos' set but not used [-Wunused-but-set-variable]
int text_mate_pos = hit_buf->core.mpos;
^~~~~~~~~~~~~
bwt_map.cpp:1486:8: warning: variable 'spliced_alignment' set but not used [-Wunused-but-set-variable]
bool spliced_alignment = false;
^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp
common.cpp: In function 'void str_appendInt(std::__cxx11::string&, int64_t)':
common.cpp:441:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
sprintf(int_str, "%ld", v);
^
common.cpp: In function 'void str_appendUInt(std::__cxx11::string&, uint64_t)':
common.cpp:447:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
sprintf(uint_str, "%lu", v);
^
common.cpp: In member function 'std::__cxx11::string GBamRecord::seqData(std::__cxx11::string*)':
common.cpp:1259:8: warning: variable 'mate_num' set but not used [-Wunused-but-set-variable]
int mate_num=0;
^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o junctions.o junctions.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o insertions.o insertions.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o deletions.o deletions.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o fusions.o fusions.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o align_status.o align_status.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o fragments.o fragments.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tokenize.o tokenize.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o inserts.o inserts.cpp
In file included from /usr/include/c++/7/vector:69:0,
from bwt_map.h:13,
from inserts.cpp:17:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = InsertAlignment; _Alloc = std::allocator<InsertAlignment>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<InsertAlignment>::iterator {aka __gnu_cxx::__normal_iterator<InsertAlignment*, std::vector<InsertAlignment> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from bwt_map.h:13,
from inserts.cpp:17:
/usr/include/c++/7/bits/stl_vector.h: In function 'void best_insert_mappings(uint64_t, ReadTable&, HitList&, HitList&, BestInsertAlignmentTable&, bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InsertAlignment*, std::vector<InsertAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InsertAlignment*, std::vector<InsertAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InsertAlignment*, std::vector<InsertAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InsertAlignment*, std::vector<InsertAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InsertAlignment*, std::vector<InsertAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InsertAlignment*, std::vector<InsertAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InsertAlignment*, std::vector<InsertAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o qual.o qual.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bam_merge_impl.o bam_merge_impl.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/c++/7/queue:61,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = CBamLine; _Alloc = std::allocator<CBamLine>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<CBamLine>::iterator {aka __gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/queue:62:0,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >; _Distance = int; _Tp = CBamLine; _Compare = __gnu_cxx::__ops::_Iter_comp_val<less_bam>]':
/usr/include/c++/7/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >; _Distance = int; _Tp = CBamLine; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less_bam>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less_bam>]':
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_heap.h: In constructor 'BamMerge::BamMerge(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<long long int>)':
/usr/include/c++/7/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
std::__make_heap(__first, __last, __cmp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/c++/7/queue:61,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from bam_merge.h:9,
from bam_merge_impl.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less_bam>]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<less_bam>]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<less_bam>]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/c++/7/queue:61,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool BamMerge::next_bam_lines(std::vector<CBamLine>&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from bam_merge.h:9,
from bam_merge_impl.cpp:1:
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/c++/7/queue:61,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CBamLine*, std::vector<CBamLine> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o utils.o utils.cpp
utils.cpp: In function 'bool calculate_offsets(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<long long unsigned int>&, std::vector<std::vector<long long int> >&)':
utils.cpp:42:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=]
sprintf(suffix, "%lu.bam", j);
^
In file included from /usr/include/c++/7/vector:69:0,
from utils.h:12,
from utils.cpp:20:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = std::pair<long long unsigned int, long long int>; _Alloc = std::allocator<std::pair<long long unsigned int, long long int> >]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, long long int> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long int>*, std::vector<std::pair<long long unsigned int, long long int> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, long long int> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long int>*, std::vector<std::pair<long long unsigned int, long long int> > >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from utils.h:12,
from utils.cpp:20:
/usr/include/c++/7/bits/stl_vector.h: In function 'void calculate_offsets_from_ids(const string&, const std::vector<long long unsigned int>&, std::vector<long long int>&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
utils.cpp:170:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
}
^
In file included from /usr/include/c++/7/vector:64:0,
from utils.h:12,
from utils.cpp:20:
/usr/include/c++/7/bits/stl_vector.h: In function 'bool calculate_offsets(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<long long unsigned int>&, std::vector<std::vector<long long int> >&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long int>*, std::vector<std::pair<long long unsigned int, long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o coverage.o coverage.cpp
coverage.cpp: In member function 'void Coverage::print_info() const':
coverage.cpp:226:96: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::map<int, std::vector<signed char> >::size_type {aka unsigned int}' [-Wformat=]
fprintf(stderr, "# of islands: %lu, # of bases covered: %lu\n", itr->second.size(), bases);
~~~~~~~~~~~~~~~~~~ ^
coverage.cpp:226:96: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=]
coverage.cpp:230:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=]
fprintf(stderr, "# of total bases: %lu\n", total_bases);
^
coverage.cpp: In member function 'void Coverage::print_info(int, const std::vector<signed char>&) const':
coverage.cpp:250:60: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector<signed char>::size_type {aka unsigned int}' [-Wformat=]
fprintf(stderr, "\tPos: %d, size: %lu\n", pos, cov.size());
~~~~~~~~~~^
rm -f libtophat.a
ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o bam_merge_impl.o utils.o coverage.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libtophat.a
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o prep_reads.o prep_reads.cpp
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o prep_reads prep_reads.o ../src/libtophat.a -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GTFToFasta.o GTFToFasta.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o FastaTools.o FastaTools.cpp
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o gtf_to_fasta GTFToFasta.o FastaTools.o ../src/libtophat.a libgc.a -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o fix_map_ordering.o fix_map_ordering.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/c++/7/queue:61,
from fix_map_ordering.cpp:11:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = std::pair<long long unsigned int, bam1_t*>; _Alloc = std::allocator<std::pair<long long unsigned int, bam1_t*> >]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, bam1_t*> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, bam1_t*>*, std::vector<std::pair<long long unsigned int, bam1_t*> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/queue:62:0,
from fix_map_ordering.cpp:11:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, bam1_t*>*, std::vector<std::pair<long long unsigned int, bam1_t*> > >; _Distance = int; _Tp = std::pair<long long unsigned int, bam1_t*>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<BamMapOrdering>]':
/usr/include/c++/7/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, bam1_t*>*, std::vector<std::pair<long long unsigned int, bam1_t*> > >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/c++/7/queue:61,
from fix_map_ordering.cpp:11:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = std::pair<long long unsigned int, TabSplitLine*>; _Alloc = std::allocator<std::pair<long long unsigned int, TabSplitLine*> >]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, TabSplitLine*> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, TabSplitLine*>*, std::vector<std::pair<long long unsigned int, TabSplitLine*> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, TabSplitLine*> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, TabSplitLine*>*, std::vector<std::pair<long long unsigned int, TabSplitLine*> > >}' changed in GCC 7.1
In file included from /usr/include/c++/7/queue:62:0,
from fix_map_ordering.cpp:11:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, TabSplitLine*>*, std::vector<std::pair<long long unsigned int, TabSplitLine*> > >; _Distance = int; _Tp = std::pair<long long unsigned int, TabSplitLine*>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<MapOrdering>]':
/usr/include/c++/7/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, TabSplitLine*>*, std::vector<std::pair<long long unsigned int, TabSplitLine*> > >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, bam1_t*>*, std::vector<std::pair<long long unsigned int, bam1_t*> > >; _Distance = int; _Tp = std::pair<long long unsigned int, bam1_t*>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<BamMapOrdering>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, bam1_t*>*, std::vector<std::pair<long long unsigned int, bam1_t*> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/c++/7/queue:61,
from fix_map_ordering.cpp:11:
/usr/include/c++/7/bits/stl_vector.h: In function 'void driver_bam(std::__cxx11::string&, GBamWriter&, GBamWriter*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, bam1_t*>*, std::vector<std::pair<long long unsigned int, bam1_t*> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, bam1_t*>*, std::vector<std::pair<long long unsigned int, bam1_t*> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, bam1_t*>*, std::vector<std::pair<long long unsigned int, bam1_t*> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/queue:62:0,
from fix_map_ordering.cpp:11:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, TabSplitLine*>*, std::vector<std::pair<long long unsigned int, TabSplitLine*> > >; _Distance = int; _Tp = std::pair<long long unsigned int, TabSplitLine*>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<MapOrdering>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, TabSplitLine*>*, std::vector<std::pair<long long unsigned int, TabSplitLine*> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/c++/7/queue:61,
from fix_map_ordering.cpp:11:
/usr/include/c++/7/bits/stl_vector.h: In function 'void driver_headerless(FILE*, FILE*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, TabSplitLine*>*, std::vector<std::pair<long long unsigned int, TabSplitLine*> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o fix_map_ordering fix_map_ordering.o ../src/libtophat.a -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bam2fastx.o bam2fastx.cpp
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o bam2fastx bam2fastx.o ../src/libgc.a -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o segment_juncs.o segment_juncs.cpp
segment_juncs.cpp: In function 'void get_seqs(std::istream&, RefSequenceTable&, bool)':
segment_juncs.cpp:84:70: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'seqan::Size<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Packed<seqan::Alloc<> > > >::Type {aka unsigned int}' [-Wformat=]
fprintf(stderr, " done (%ld bases).\n", seqan::length(*ref_str));
~~~~~~~~~~~~~~~~~~~~~~~^
segment_juncs.cpp: In member function 'void SegmentSearchWorker::operator()()':
segment_juncs.cpp:4625:27: warning: variable 'last_read_id' set but not used [-Wunused-but-set-variable]
uint64_t read_id = 0, last_read_id = 0;
^~~~~~~~~~~~
segment_juncs.cpp: In function 'void driver(std::istream&, FILE*, FILE*, FILE*, FILE*, std::__cxx11::string&, std::__cxx11::string&, std::vector<std::__cxx11::basic_string<char> >&, std::__cxx11::string&, std::__cxx11::string&, std::vector<std::__cxx11::basic_string<char> >&)':
segment_juncs.cpp:5063:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::set<Junction>::size_type {aka unsigned int}' [-Wformat=]
fprintf(stderr, "Reporting %lu potential deletions...\n", deletions.size());
~~~~~~~~~~~~~~~~^
segment_juncs.cpp:5081:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::set<Insertion>::size_type {aka unsigned int}' [-Wformat=]
fprintf(stderr, "Reporting %lu potential insertions...\n", insertions.size());
~~~~~~~~~~~~~~~~~^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/boost/thread/pthread/thread_data.hpp:24,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from segment_juncs.cpp:16:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/boost/thread/pthread/thread_data.hpp:24,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from segment_juncs.cpp:16:
/usr/include/c++/7/bits/stl_vector.h: In function 'size_t index_read(MerTable*, int, const string&, unsigned int, bool, std::vector<long long unsigned int>&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/boost/thread/pthread/thread_data.hpp:24,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from segment_juncs.cpp:16:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = HitsForRead; _Alloc = std::allocator<HitsForRead>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<HitsForRead>::iterator {aka __gnu_cxx::__normal_iterator<HitsForRead*, std::vector<HitsForRead> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/boost/thread/pthread/thread_data.hpp:24,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from segment_juncs.cpp:16:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void RecordButterflyJuncs::record(uint32_t, const std::vector<std::pair<unsigned int, DnaSpliceStrings> >&, const std::vector<std::pair<unsigned int, DnaSpliceStrings> >&, bool, PotentialJuncs&, int, int, size_t, size_t)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void find_gaps(RefSequenceTable&, ReadStream&, std::vector<HitsForRead>&, HitStream&, HitStream&, std::set<Junction, skip_count_lt>&, eREAD)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HitsForRead*, std::vector<HitsForRead> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void driver(std::istream&, FILE*, FILE*, FILE*, FILE*, std::__cxx11::string&, std::__cxx11::string&, std::vector<std::__cxx11::basic_string<char> >&, std::__cxx11::string&, std::__cxx11::string&, std::vector<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o segment_juncs segment_juncs.o ../src/libtophat.a -lboost_thread -lboost_system -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gtf_juncs.o gtf_juncs.cpp
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o gtf_juncs gtf_juncs.o ../src/libtophat.a libgc.a -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o juncs_db.o juncs_db.cpp
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o juncs_db juncs_db.o ../src/libtophat.a -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o long_spanning_reads.o long_spanning_reads.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/boost/thread/pthread/thread_data.hpp:24,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from long_spanning_reads.cpp:16:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = std::reverse_iterator<__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> > >; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = HitsForRead; _Alloc = std::allocator<HitsForRead>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<HitsForRead>::iterator {aka __gnu_cxx::__normal_iterator<HitsForRead*, std::vector<HitsForRead> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/boost/thread/pthread/thread_data.hpp:24,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from long_spanning_reads.cpp:16:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void JoinSegmentsWorker::operator()()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HitsForRead*, std::vector<HitsForRead> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HitsForRead*, std::vector<HitsForRead> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void driver(const string&, std::istream&, std::vector<_IO_FILE*>&, std::vector<_IO_FILE*>&, std::vector<_IO_FILE*>&, std::vector<_IO_FILE*>&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, const string&)':
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o long_spanning_reads long_spanning_reads.o ../src/libtophat.a -lboost_thread -lboost_system -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bam_merge.o bam_merge.cpp
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o bam_merge bam_merge.o ../src/libtophat.a ../src/libgc.a -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o map2gtf.o map2gtf.cpp
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o map2gtf map2gtf.o ../src/libtophat.a libgc.a -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tophat_reports.o tophat_reports.cpp
tophat_reports.cpp: In constructor 'MultipleBAMReader::MultipleBAMReader(ReadTable&, RefSequenceTable&, const std::vector<std::__cxx11::basic_string<char> >&, long int, long int)':
tophat_reports.cpp:1806:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=]
sprintf(suffix, "%lu.bam", j);
^
tophat_reports.cpp: In function 'void print_alnStats(SAlignStats&)':
tophat_reports.cpp:2131:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
fprintf(f, " Input : %9ld\n", total_left);
^
tophat_reports.cpp:2134:35: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
alnStats.num_aligned_left, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~ ^
tophat_reports.cpp:2138:90: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
alnStats.num_aligned_left_multi, perc, alnStats.num_aligned_left_xmulti, max_multihits);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
tophat_reports.cpp:2138:90: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t {aka long long int}' [-Wformat=]
tophat_reports.cpp:2149:57: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
fprintf(f, " Input : %9ld\n", total_right);
^
tophat_reports.cpp:2153:37: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
alnStats.num_aligned_right, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
tophat_reports.cpp:2157:94: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
alnStats.num_aligned_right_multi, perc, alnStats.num_aligned_right_xmulti, max_multihits);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
tophat_reports.cpp:2157:94: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t {aka long long int}' [-Wformat=]
tophat_reports.cpp:2164:62: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
fprintf(f, " Input : %9ld\n", total_unpaired);
^
tophat_reports.cpp:2168:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
alnStats.num_aligned_unpaired, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
tophat_reports.cpp:2172:102: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
alnStats.num_aligned_unpaired_multi, perc, alnStats.num_aligned_unpaired_xmulti, max_multihits);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
tophat_reports.cpp:2172:102: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t {aka long long int}' [-Wformat=]
tophat_reports.cpp:2180:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
fprintf(f, "\nAligned pairs: %9ld\n", alnStats.num_aligned_pairs);
~~~~~~~~~~~~~~~~~~~~~~~~~~^
tophat_reports.cpp:2184:43: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
alnStats.num_aligned_pairs_multi, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
tophat_reports.cpp:2189:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat=]
alnStats.num_aligned_pairs_disc, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/boost/thread/pthread/thread_data.hpp:24,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from tophat_reports.cpp:19:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/boost/thread/pthread/thread_data.hpp:24,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from tophat_reports.cpp:19:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'MultipleBAMReader::MultipleBAMReader(ReadTable&, RefSequenceTable&, const std::vector<std::__cxx11::basic_string<char> >&, long int, long int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o tophat_reports tophat_reports.o ../src/libtophat.a -lboost_thread -lboost_system -lbam -lz
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o sam_juncs.o sam_juncs.cpp
sam_juncs.cpp: In function 'void driver(FILE*)':
sam_juncs.cpp:106:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::map<Junction, JunctionStats>::size_type {aka unsigned int}' [-Wformat=]
fprintf(stderr, "Extracted %lu junctions\n", junctions.size());
~~~~~~~~~~~~~~~~^
g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -o sam_juncs sam_juncs.o ../src/libtophat.a -lbam -lz
cp tophat2.sh tophat2 && chmod 755 tophat2
sed -e 's|__VERSION__|2.1.1|' tophat.py > tophat && chmod 755 tophat
make[3]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
make[3]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[3]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[2]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_auto_test -a -O--no-parallel
make -j1 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
make[2]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[2]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --no-parallel
dh_testroot -a -O--no-parallel
dh_prep -a -O--no-parallel
dh_auto_install -a -O--no-parallel
make -j1 install DESTDIR=/<<BUILDDIR>>/tophat-2.1.1\+dfsg1/debian/tophat AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
Making install in src
make[2]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
make[3]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
/bin/mkdir -p '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin'
/usr/bin/install -c prep_reads gtf_to_fasta fix_map_ordering bam2fastx segment_juncs gtf_juncs juncs_db long_spanning_reads bam_merge map2gtf tophat_reports sam_juncs '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin'
/usr/bin/install -c tophat2 tophat '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin'
/usr/bin/install -c contig_to_chr_coords bed_to_juncs sra_to_solid tophat-fusion-post '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
make[2]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
make[2]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[3]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[2]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_installdocs -a -O--no-parallel
dh_installchangelogs -a -O--no-parallel
debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_installman
# try to create man pages whereever possible
mkdir -p /<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1
help2man --no-info --no-discard-stderr -h "" \
--name='tophat component converting bam directly into fastx' \
--version-string="2.1.1+dfsg1-1" \
/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin/bam2fastx > /<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1/bam2fastx.1
help2man --no-info --no-discard-stderr -h "-h" \
--name='tophat component to convert junctions in BED format' \
--version-string="2.1.1+dfsg1-1" \
/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin/bed_to_juncs > /<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1/bed_to_juncs.1
help2man --no-info --no-discard-stderr -h "-h" \
--name='tophat component taking NCBI seq_contig file and maps contig coords' \
--version-string="2.1.1+dfsg1-1" \
/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin/contig_to_chr_coords > /<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1/contig_to_chr_coords.1
help2man --no-info --no-discard-stderr \
--name='TopHat maps short sequences from spliced transcripts to whole genomes' \
--version-string="2.1.1+dfsg1-1" \
/<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/bin/tophat > /<<BUILDDIR>>/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1/tophat.1
make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_perl -a -O--no-parallel
dh_link -a -O--no-parallel
dh_strip_nondeterminism -a -O--no-parallel
dh_compress -a -O--no-parallel
dh_fixperms -a -O--no-parallel
dh_missing -a -O--no-parallel
dh_strip -a -O--no-parallel
dh_makeshlibs -a -O--no-parallel
dh_shlibdeps -a -O--no-parallel
dpkg-shlibdeps: warning: debian/tophat/usr/bin/gtf_to_fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/long_spanning_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/juncs_db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/gtf_juncs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/tophat_reports contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/map2gtf contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/bam2fastx contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/bam_merge contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/sam_juncs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/fix_map_ordering contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/segment_juncs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tophat/usr/bin/prep_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tophat/usr/bin/gtf_to_fasta debian/tophat/usr/bin/long_spanning_reads debian/tophat/usr/bin/juncs_db debian/tophat/usr/bin/gtf_juncs debian/tophat/usr/bin/tophat_reports debian/tophat/usr/bin/map2gtf debian/tophat/usr/bin/bam2fastx debian/tophat/usr/bin/bam_merge debian/tophat/usr/bin/sam_juncs debian/tophat/usr/bin/fix_map_ordering debian/tophat/usr/bin/segment_juncs debian/tophat/usr/bin/prep_reads were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--no-parallel
dh_gencontrol -a -O--no-parallel
dh_md5sums -a -O--no-parallel
dh_builddeb -a -O--no-parallel
dpkg-deb: building package 'tophat' in '../tophat_2.1.1+dfsg1-1_armhf.deb'.
dpkg-deb: building package 'tophat-dbgsym' in '../tophat-dbgsym_2.1.1+dfsg1-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../tophat_2.1.1+dfsg1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build tophat-2.1.1+dfsg1
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-12-13T07:26:49Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
tophat_2.1.1+dfsg1-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 06 Dec 2017 16:13:31 +0100
Source: tophat
Binary: tophat
Architecture: armhf
Version: 2.1.1+dfsg1-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Fabian Klötzl <fabian@kloetzl.info>
Description:
tophat - fast splice junction mapper for RNA-Seq reads
Closes: 780816
Changes:
tophat (2.1.1+dfsg1-1) unstable; urgency=medium
.
* Team upload
.
* debian/upstream/metadata:
- Added references to registries
- yamllint cleanliness
.
[ Nadiya Sitdykova ]
* add info about debian/tests/test_data
.
[ Fabian Klötzl ]
* remove convenience copy of samtools.
Closes: #780816
* adapt tophat script to recent samtools version
.
[ Andreas Tille ]
* Remove unused license paragraph
* Standards-Version: 4.1.1
* Really remove samtools code copy also from source tarball
* Versioned Depends: samtools (>= 1.5)
* d/watch: enable numbered dfsg-appendices
Checksums-Sha1:
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14cea5c1035428f5c028f96aeb2ffd418c76934f 5617 tophat_2.1.1+dfsg1-1_armhf.buildinfo
da971125a473e8b3d33e4e2f7439b08fdc43a145 518492 tophat_2.1.1+dfsg1-1_armhf.deb
Checksums-Sha256:
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68c13457c014dd545a239fcfb898c76e8cd0e4b04d909865c373c802605f8cf4 5617 tophat_2.1.1+dfsg1-1_armhf.buildinfo
2d065732e5c0fb0d365aac670f989998bae2c0f1abc9dd83f604de1991569518 518492 tophat_2.1.1+dfsg1-1_armhf.deb
Files:
0f12b389c136c3d70dad6056d7b33e3b 6989004 debug optional tophat-dbgsym_2.1.1+dfsg1-1_armhf.deb
a501d94205c256440352909dcfe90393 5617 science optional tophat_2.1.1+dfsg1-1_armhf.buildinfo
1677d9fc1da35f91ab4a2c0c79d89dac 518492 science optional tophat_2.1.1+dfsg1-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
tophat-dbgsym_2.1.1+dfsg1-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 6989004 bytes: control archive=1096 bytes.
830 bytes, 12 lines control
1272 bytes, 12 lines md5sums
Package: tophat-dbgsym
Source: tophat
Version: 2.1.1+dfsg1-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7440
Depends: tophat (= 2.1.1+dfsg1-1)
Section: debug
Priority: optional
Description: debug symbols for tophat
Build-Ids: 18ec661a72830d7f8223bad31e5e4db92c20ce70 1e0edfb97e885afc43e89210aeb6997ca649f16b 2b3d77ad591430477044fd76b0d88cd648a38f2a 44c5aeca699c876d8955391a78ac02610d36f74b 528f7225d8711e92066c3944d2f861db750a72ec 5f2f0f1a0d7f964c11f6c56c114c9e8ab4187cdb 67aa431cb09858e4615269266cf9ef0142387c44 78138b16553b00746ef71a5c3ee44d3d8f03fd52 8b6ed38ab015bce1d1dc9c24b550b72ddcde468d b14ec46577f089b270524d5cbf16ca530858793c cf4798884c6b030f89c65fda864e9d71efed6f09 e10cfe3b931c0ad4151f5e9d1083f134dad9940b
drwxr-xr-x root/root 0 2017-12-06 15:13 ./
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/18/
-rw-r--r-- root/root 257844 2017-12-06 15:13 ./usr/lib/debug/.build-id/18/ec661a72830d7f8223bad31e5e4db92c20ce70.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/1e/
-rw-r--r-- root/root 191756 2017-12-06 15:13 ./usr/lib/debug/.build-id/1e/0edfb97e885afc43e89210aeb6997ca649f16b.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/2b/
-rw-r--r-- root/root 1859472 2017-12-06 15:13 ./usr/lib/debug/.build-id/2b/3d77ad591430477044fd76b0d88cd648a38f2a.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/44/
-rw-r--r-- root/root 330924 2017-12-06 15:13 ./usr/lib/debug/.build-id/44/c5aeca699c876d8955391a78ac02610d36f74b.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/52/
-rw-r--r-- root/root 369720 2017-12-06 15:13 ./usr/lib/debug/.build-id/52/8f7225d8711e92066c3944d2f861db750a72ec.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/5f/
-rw-r--r-- root/root 346768 2017-12-06 15:13 ./usr/lib/debug/.build-id/5f/2f0f1a0d7f964c11f6c56c114c9e8ab4187cdb.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/67/
-rw-r--r-- root/root 161700 2017-12-06 15:13 ./usr/lib/debug/.build-id/67/aa431cb09858e4615269266cf9ef0142387c44.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/78/
-rw-r--r-- root/root 1372932 2017-12-06 15:13 ./usr/lib/debug/.build-id/78/138b16553b00746ef71a5c3ee44d3d8f03fd52.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/8b/
-rw-r--r-- root/root 647036 2017-12-06 15:13 ./usr/lib/debug/.build-id/8b/6ed38ab015bce1d1dc9c24b550b72ddcde468d.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/b1/
-rw-r--r-- root/root 61032 2017-12-06 15:13 ./usr/lib/debug/.build-id/b1/4ec46577f089b270524d5cbf16ca530858793c.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/cf/
-rw-r--r-- root/root 1694880 2017-12-06 15:13 ./usr/lib/debug/.build-id/cf/4798884c6b030f89c65fda864e9d71efed6f09.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root 297572 2017-12-06 15:13 ./usr/lib/debug/.build-id/e1/0cfe3b931c0ad4151f5e9d1083f134dad9940b.debug
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/share/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-12-06 15:13 ./usr/share/doc/tophat-dbgsym -> tophat
tophat_2.1.1+dfsg1-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 518492 bytes: control archive=1932 bytes.
930 bytes, 18 lines control
2672 bytes, 40 lines md5sums
Package: tophat
Version: 2.1.1+dfsg1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3095
Depends: libboost-system1.62.0, libboost-thread1.62.0, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), python, bowtie2 | bowtie, samtools (>= 1.5)
Suggests: cufflinks
Section: science
Priority: optional
Homepage: http://ccb.jhu.edu/software/tophat
Description: fast splice junction mapper for RNA-Seq reads
TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra
high-throughput short read aligner Bowtie, and then analyzes the
mapping results to identify splice junctions between exons.
TopHat is a collaborative effort between the University of Maryland
Center for Bioinformatics and Computational Biology and the
University of California, Berkeley Departments of Mathematics and
Molecular and Cell Biology.
drwxr-xr-x root/root 0 2017-12-06 15:13 ./
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/bin/
-rwxr-xr-x root/root 109256 2017-12-06 15:13 ./usr/bin/bam2fastx
-rwxr-xr-x root/root 139136 2017-12-06 15:13 ./usr/bin/bam_merge
-rwxr-xr-x root/root 1925 2017-12-06 15:13 ./usr/bin/bed_to_juncs
-rwxr-xr-x root/root 4631 2017-12-06 15:13 ./usr/bin/contig_to_chr_coords
-rwxr-xr-x root/root 139136 2017-12-06 15:13 ./usr/bin/fix_map_ordering
-rwxr-xr-x root/root 204688 2017-12-06 15:13 ./usr/bin/gtf_juncs
-rwxr-xr-x root/root 221072 2017-12-06 15:13 ./usr/bin/gtf_to_fasta
-rwxr-xr-x root/root 159620 2017-12-06 15:13 ./usr/bin/juncs_db
-rwxr-xr-x root/root 384896 2017-12-06 15:13 ./usr/bin/long_spanning_reads
-rwxr-xr-x root/root 159616 2017-12-06 15:13 ./usr/bin/map2gtf
-rwxr-xr-x root/root 188816 2017-12-06 15:13 ./usr/bin/prep_reads
-rwxr-xr-x root/root 229248 2017-12-06 15:13 ./usr/bin/sam_juncs
-rwxr-xr-x root/root 434316 2017-12-06 15:13 ./usr/bin/segment_juncs
-rwxr-xr-x root/root 716 2017-12-06 15:13 ./usr/bin/sra_to_solid
-rwxr-xr-x root/root 171670 2017-12-06 15:13 ./usr/bin/tophat
-rwxr-xr-x root/root 118409 2017-12-06 15:13 ./usr/bin/tophat-fusion-post
-rwxr-xr-x root/root 166 2017-12-06 15:13 ./usr/bin/tophat2
-rwxr-xr-x root/root 434048 2017-12-06 15:13 ./usr/bin/tophat_reports
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/share/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/share/doc/tophat/
-rw-r--r-- root/root 789 2016-02-14 18:21 ./usr/share/doc/tophat/README
-rw-r--r-- root/root 261 2017-12-06 15:13 ./usr/share/doc/tophat/README.test
-rw-r--r-- root/root 3248 2017-12-06 15:13 ./usr/share/doc/tophat/changelog.Debian.gz
-rw-r--r-- root/root 2723 2017-12-06 15:13 ./usr/share/doc/tophat/copyright
-rw-r--r-- root/root 266 2017-12-06 15:13 ./usr/share/doc/tophat/run-unit-test
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/
-rw-r--r-- root/root 1870 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/reads_1.fq.gz
-rw-r--r-- root/root 1863 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/reads_2.fq.gz
-rw-r--r-- root/root 5283 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.1.bt2.gz
-rw-r--r-- root/root 5274 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.1.ebwt.gz
-rw-r--r-- root/root 168 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.2.bt2
-rw-r--r-- root/root 88 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.2.ebwt
-rw-r--r-- root/root 17 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.3.bt2
-rw-r--r-- root/root 163 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.4.bt2
-rw-r--r-- root/root 680 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.fa
-rw-r--r-- root/root 5285 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.rev.1.bt2.gz
-rw-r--r-- root/root 5268 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.rev.1.ebwt.gz
-rw-r--r-- root/root 168 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.rev.2.bt2
-rw-r--r-- root/root 88 2017-12-06 15:13 ./usr/share/doc/tophat/test_data/test_ref.rev.2.ebwt
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/share/man/
drwxr-xr-x root/root 0 2017-12-06 15:13 ./usr/share/man/man1/
-rw-r--r-- root/root 1059 2017-12-06 15:13 ./usr/share/man/man1/bam2fastx.1.gz
-rw-r--r-- root/root 320 2017-12-06 15:13 ./usr/share/man/man1/bed_to_juncs.1.gz
-rw-r--r-- root/root 353 2017-12-06 15:13 ./usr/share/man/man1/contig_to_chr_coords.1.gz
-rw-r--r-- root/root 1914 2017-12-06 15:13 ./usr/share/man/man1/tophat.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 93080
Build-Time: 412
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 190
Job: tophat_2.1.1+dfsg1-1
Machine Architecture: armhf
Package: tophat
Package-Time: 618
Source-Version: 2.1.1+dfsg1-1
Space: 93080
Status: successful
Version: 2.1.1+dfsg1-1
--------------------------------------------------------------------------------
Finished at 2017-12-13T07:26:49Z
Build needed 00:10:18, 93080k disk space