tophat →
2.1.1+dfsg1-2 →
armhf → 2018-08-20 06:29:01
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| tophat 2.1.1+dfsg1-2 (armhf) Mon, 20 Aug 2018 05:58:26 +0000 |
+==============================================================================+
Package: tophat
Version: 2.1.1+dfsg1-2
Source Version: 2.1.1+dfsg1-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-4e5cda1d-89a1-4cc7-a94b-7c3a056eec64' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.7 MB]
Fetched 23.7 MB in 26s (904 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://salsa.debian.org/med-team/tophat.git
Please use:
git clone https://salsa.debian.org/med-team/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+dfsg1-2 (dsc) [2184 B]
Get:2 http://172.17.0.1/private buster-staging/main tophat 2.1.1+dfsg1-2 (tar) [350 kB]
Get:3 http://172.17.0.1/private buster-staging/main tophat 2.1.1+dfsg1-2 (diff) [18.6 kB]
Fetched 371 kB in 0s (4044 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tophat-eLUFBm/tophat-2.1.1+dfsg1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tophat-eLUFBm' 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-rt4NdD/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-rt4NdD/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-rt4NdD/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2950 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 7 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15689 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), libbam-dev, zlib1g-dev, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man, bowtie
Filtered Build-Depends: debhelper (>= 11~), 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-rt4NdD/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-rt4NdD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ Sources [546 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ Packages [625 B]
Fetched 2504 B in 1s (3661 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 dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bowtie bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl 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 libelf1 libfile-stripnondeterminism-perl
libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0
libicu60 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support
po-debconf python python-minimal python2 python2-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 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 apparmor less
www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bowtie bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl 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 libelf1 libfile-stripnondeterminism-perl
libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0
libicu60 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support
po-debconf python python-minimal python2 python2-minimal python2.7
python2.7-minimal sbuild-build-depends-tophat-dummy seqan-dev zlib1g-dev
0 upgraded, 68 newly installed, 0 to remove and 7 not upgraded.
Need to get 34.8 MB/35.4 MB of archives.
After this operation, 220 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-rt4NdD/apt_archive ./ sbuild-build-depends-tophat-dummy 0.invalid.0 [908 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b2 [18.3 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-3 [393 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-3 [1082 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-3 [1843 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-3 [298 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 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 20180224.1 [77.0 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1 [771 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 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 0.042-1 [12.1 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.7-1 [856 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.6 [169 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-4 [111 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-8 [7003 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libboost-atomic1.62.0 armhf 1.62.0+dfsg-8 [31.8 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libboost-atomic1.62-dev armhf 1.62.0+dfsg-8 [30.2 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libboost-system1.62.0 armhf 1.62.0+dfsg-8 [32.8 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libboost-chrono1.62.0 armhf 1.62.0+dfsg-8 [36.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libboost-chrono1.62-dev armhf 1.62.0+dfsg-8 [38.1 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libboost-date-time1.62.0 armhf 1.62.0+dfsg-8 [41.9 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.62.0 armhf 1.62.0+dfsg-8 [106 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.62-dev armhf 1.62.0+dfsg-8 [172 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libboost-date-time1.62-dev armhf 1.62.0+dfsg-8 [52.0 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libboost-system1.62-dev armhf 1.62.0+dfsg-8 [33.8 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libboost-thread1.62.0 armhf 1.62.0+dfsg-8 [65.6 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libboost-thread1.62-dev armhf 1.62.0+dfsg-8 [72.4 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf seqan-dev all 1.4.2+dfsg-3 [1096 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf bowtie armhf 1.0.0-5 [1320 kB]
debconf: delaying package configuration, since apt-utils is not installed
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.1.0-12+rpi1 gcc-8_8.1.0-12+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bowtie_1.0.0-5 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.1.0-12+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.1.0-12+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 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libboost-atomic1.62.0_1.62.0+dfsg-8 libboost-chrono1.62-dev_1.62.0+dfsg-8 libboost-chrono1.62.0_1.62.0+dfsg-8 libboost-date-time1.62-dev_1.62.0+dfsg-8 libboost-date-time1.62.0_1.62.0+dfsg-8 libboost-serialization1.62-dev_1.62.0+dfsg-8 libboost-serialization1.62.0_1.62.0+dfsg-8 libboost-system-dev_1.62.0.1+b8 libboost-system1.62-dev_1.62.0+dfsg-8 libboost-system1.62.0_1.62.0+dfsg-8 libboost-thread-dev_1.62.0.1+b8 libboost-thread1.62-dev_1.62.0+dfsg-8 libboost-thread1.62.0_1.62.0+dfsg-8 libboost1.62-dev_1.62.0+dfsg-8 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-12+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.1.0-12+rpi1 libgcc1_1:8.1.0-12+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.1.0-12+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.11-2 libharfbuzz0b_1.8.7-1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-7 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-10 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-3 libpython2.7-stdlib_2.7.15-3 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 libsystemd0_239-7 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-2.1 libubsan1_8.1.0-12+rpi1 libudev1_239-7 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-3 python2.7-minimal_2.7.15-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tophat-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 seqan-dev_1.4.2+dfsg-3 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Aug 18 07:33:00 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./tophat_2.1.1+dfsg1-2.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+dfsg1-2.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
dpkg-source: info: applying fix_makefile.am.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-4e5cda1d-89a1-4cc7-a94b-7c3a056eec64
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package tophat
dpkg-buildpackage: info: source version 2.1.1+dfsg1-2
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 --runstatedir=/run --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 whether make supports the include directive... yes (GNU style)
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 8.1.0-12+rpi1) 8.1.0
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 prep_reads.o prep_reads.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 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:441:20: 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:447:21: 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++/8/vector:69,
from bwt_map.h:13,
from inserts.cpp:17:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = InsertAlignment; _Alloc = std::allocator<InsertAlignment>]':
/usr/include/c++/8/bits/vector.tcc:418:5: 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++/8/vector:64,
from bwt_map.h:13,
from inserts.cpp:17:
/usr/include/c++/8/bits/stl_vector.h: In function 'void best_insert_mappings(uint64_t, ReadTable&, HitList&, HitList&, BestInsertAlignmentTable&, bool)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/vector:69,
from /usr/include/c++/8/queue:61,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = CBamLine; _Alloc = std::allocator<CBamLine>]':
/usr/include/c++/8/bits/vector.tcc:418:5: 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++/8/queue:62,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/bits/stl_heap.h: In constructor 'BamMerge::BamMerge(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<long long int>)':
/usr/include/c++/8/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++/8/vector:64,
from /usr/include/c++/8/queue:61,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/algorithm:62,
from bam_merge.h:9,
from bam_merge_impl.cpp:1:
/usr/include/c++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/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++/8/vector:64,
from /usr/include/c++/8/queue:61,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool BamMerge::next_bam_lines(std::vector<CBamLine>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/algorithm:62,
from bam_merge.h:9,
from bam_merge_impl.cpp:1:
/usr/include/c++/8/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++/8/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++/8/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++/8/vector:64,
from /usr/include/c++/8/queue:61,
from bam_merge.h:8,
from bam_merge_impl.cpp:1:
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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:42:24: 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++/8/vector:69,
from utils.h:12,
from utils.cpp:20:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = std::pair<long long unsigned int, long long int>; _Alloc = std::allocator<std::pair<long long unsigned int, long long int> >]':
/usr/include/c++/8/bits/vector.tcc:418:5: 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:418:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:418:5: 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++/8/vector:64,
from utils.h:12,
from utils.cpp:20:
/usr/include/c++/8/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++/8/bits/stl_vector.h:1085:4: 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++/8/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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
utils.cpp:129:1: 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
}
^
utils.cpp:129:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
utils.cpp:129:1: 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
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:226:23: 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:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
coverage.cpp:230:19: 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:250:19: 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++ -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 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++ -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
In file included from GList.hh:8,
from GFaSeqGet.h:3,
from gff.h:10,
from gff.cpp:1:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GffCDSeg]':
GVec.hh:436:5: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GffCDSeg]'
GVec.hh:81:38: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GffCDSeg]'
GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GffCDSeg]'
GList.hh:51:42: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GffCDSeg]'
gff.cpp:2117:22: required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GffCDSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:427:7: note: 'class GffCDSeg' declared here
class GffCDSeg:public GSeg {
^~~~~~~~
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++ -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 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++/8/vector:69,
from /usr/include/c++/8/queue:61,
from fix_map_ordering.cpp:11:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = std::pair<long long unsigned int, bam1_t*>; _Alloc = std::allocator<std::pair<long long unsigned int, bam1_t*> >]':
/usr/include/c++/8/bits/vector.tcc:418:5: 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++/8/queue:62,
from fix_map_ordering.cpp:11:
/usr/include/c++/8/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++/8/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++/8/vector:69,
from /usr/include/c++/8/queue:61,
from fix_map_ordering.cpp:11:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = std::pair<long long unsigned int, TabSplitLine*>; _Alloc = std::allocator<std::pair<long long unsigned int, TabSplitLine*> >]':
/usr/include/c++/8/bits/vector.tcc:418:5: 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>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/queue:62,
from fix_map_ordering.cpp:11:
/usr/include/c++/8/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++/8/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++/8/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++/8/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++/8/vector:64,
from /usr/include/c++/8/queue:61,
from fix_map_ordering.cpp:11:
/usr/include/c++/8/bits/stl_vector.h: In function 'void driver_bam(std::__cxx11::string&, GBamWriter&, GBamWriter*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/bits/stl_vector.h:1085:4: 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++/8/queue:62,
from fix_map_ordering.cpp:11:
/usr/include/c++/8/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++/8/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++/8/vector:64,
from /usr/include/c++/8/queue:61,
from fix_map_ordering.cpp:11:
/usr/include/c++/8/bits/stl_vector.h: In function 'void driver_headerless(FILE*, FILE*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: 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 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:84:23: 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:5063:19: 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:5081:19: 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++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:418:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:672:7: 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++/8/bits/vector.tcc:672:7: 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++/8/bits/vector.tcc:672:7: 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = HitsForRead; _Alloc = std::allocator<HitsForRead>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
segment_juncs.cpp:2048:3: 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
}
^
segment_juncs.cpp:2048:3: 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
segment_juncs.cpp:2048:3: 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
segment_juncs.cpp:2048:3: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /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++/8/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++/8/bits/stl_vector.h:867:4: 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++/8/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++/8/bits/stl_vector.h:1549:4: 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,
^~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1549:4: 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++/8/bits/stl_vector.h:1549:4: 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,
^~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1549:4: 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 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 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 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++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:672:7: 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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = HitsForRead; _Alloc = std::allocator<HitsForRead>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'void JoinSegmentsWorker::operator()()':
/usr/include/c++/8/bits/stl_vector.h:867:4: 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++/8/bits/stl_vector.h:867:4: 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++/8/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++/8/bits/stl_vector.h:1549:4: 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,
^~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1549:4: 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,
^~~~~~~~~~~~~~~
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 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 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 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:1806:23: 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:2131:13: 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:2133:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=]
fprintf(f, " Mapped : %9ld (%4.1f%% of input)\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alnStats.num_aligned_left, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~
tophat_reports.cpp:2137:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=]
fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alnStats.num_aligned_left_multi, perc, alnStats.num_aligned_left_xmulti, max_multihits);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tophat_reports.cpp:2137:13: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=]
tophat_reports.cpp:2149:14: 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:2152:14: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=]
fprintf(f, " Mapped : %9ld (%4.1f%% of input)\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alnStats.num_aligned_right, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~~
tophat_reports.cpp:2156:14: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=]
fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alnStats.num_aligned_right_multi, perc, alnStats.num_aligned_right_xmulti, max_multihits);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tophat_reports.cpp:2156:14: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=]
tophat_reports.cpp:2164:16: 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:2167:16: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=]
fprintf(f, " Mapped : %9ld (%4.1f%% of input)\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alnStats.num_aligned_unpaired, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tophat_reports.cpp:2171:16: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=]
fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alnStats.num_aligned_unpaired_multi, perc, alnStats.num_aligned_unpaired_xmulti, max_multihits);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tophat_reports.cpp:2171:16: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=]
tophat_reports.cpp:2180:14: 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:2183:16: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=]
fprintf(f, " of these: %9ld (%4.1f%%) have multiple alignments\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alnStats.num_aligned_pairs_multi, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tophat_reports.cpp:2188:16: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=]
fprintf(f, " %9ld (%4.1f%%) are discordant alignments\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
alnStats.num_aligned_pairs_disc, perc);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:418:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:418:5: 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++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long 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 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:106:18: 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 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+dfsg1-2" \
/<<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+dfsg1-2" \
/<<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+dfsg1-2" \
/<<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+dfsg1-2" \
/<<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/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/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/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/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/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: 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/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/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/long_spanning_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/fix_map_ordering debian/tophat/usr/bin/juncs_db debian/tophat/usr/bin/bam_merge debian/tophat/usr/bin/sam_juncs debian/tophat/usr/bin/gtf_juncs debian/tophat/usr/bin/segment_juncs debian/tophat/usr/bin/prep_reads debian/tophat/usr/bin/map2gtf debian/tophat/usr/bin/tophat_reports debian/tophat/usr/bin/bam2fastx debian/tophat/usr/bin/long_spanning_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+dfsg1-2_armhf.deb'.
dpkg-deb: building package 'tophat-dbgsym' in '../tophat-dbgsym_2.1.1+dfsg1-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../tophat_2.1.1+dfsg1-2_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 2018-08-20T06:28:51Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
tophat_2.1.1+dfsg1-2_armhf.changes:
-----------------------------------
Format: 1.8
Date: Sat, 18 Aug 2018 09:28:30 +0200
Source: tophat
Binary: tophat
Architecture: armhf
Version: 2.1.1+dfsg1-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
tophat - fast splice junction mapper for RNA-Seq reads
Closes: 906510
Changes:
tophat (2.1.1+dfsg1-2) unstable; urgency=medium
.
* Fix Makefile.am
Closes: #906510
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.0
* Remove unneeded get-orig-source target
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
tophat-dbgsym_2.1.1+dfsg1-2_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 10051548 bytes: control archive=1096 bytes.
831 bytes, 12 lines control
1272 bytes, 12 lines md5sums
Package: tophat-dbgsym
Source: tophat
Version: 2.1.1+dfsg1-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10476
Depends: tophat (= 2.1.1+dfsg1-2)
Section: debug
Priority: optional
Description: debug symbols for tophat
Build-Ids: 083e9ad7e8e53d0fbaf9a7407ce5aefe121aee91 3bb70096397c534666efae9ae24aff7066d333c7 3c256d59ce30d87f71058af744fb701fe160fe6e 5456f29cbddfa30986e880d54aec5e224701ee60 55580efc0140aca1c0a236ced5905de3e3ffc97c 5bb4d514ce65d67eb5650b3b998ba83d7f18739a 80a70013f9b2281fcc9ec63e36503dc29df3578c 8bbe4ab8b1e7d20ed28e3f805ca5d61e932c306a ae730aef84a4f84ea02a749a0f512a314d82795f cdd18ef483e53ec99fac33a647ffdd01e5c4a560 cf2342a47fc7a5727340ea9bcd3d356ea359421b e1f995f342f3dac1f71728e451368cb477d40336
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-rw-r--r-- root/root 80892 2018-08-18 07:28 ./usr/lib/debug/.build-id/80/a70013f9b2281fcc9ec63e36503dc29df3578c.debug
drwxr-xr-x root/root 0 2018-08-18 07:28 ./usr/lib/debug/.build-id/8b/
-rw-r--r-- root/root 404752 2018-08-18 07:28 ./usr/lib/debug/.build-id/8b/be4ab8b1e7d20ed28e3f805ca5d61e932c306a.debug
drwxr-xr-x root/root 0 2018-08-18 07:28 ./usr/lib/debug/.build-id/ae/
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-rw-r--r-- root/root 947572 2018-08-18 07:28 ./usr/lib/debug/.build-id/e1/f995f342f3dac1f71728e451368cb477d40336.debug
drwxr-xr-x root/root 0 2018-08-18 07:28 ./usr/share/
drwxr-xr-x root/root 0 2018-08-18 07:28 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-08-18 07:28 ./usr/share/doc/tophat-dbgsym -> tophat
tophat_2.1.1+dfsg1-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 520100 bytes: control archive=1928 bytes.
930 bytes, 18 lines control
2672 bytes, 40 lines md5sums
Package: tophat
Version: 2.1.1+dfsg1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3111
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 2018-08-18 07:28 ./
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drwxr-xr-x root/root 0 2018-08-18 07:28 ./usr/bin/
-rwxr-xr-x root/root 113352 2018-08-18 07:28 ./usr/bin/bam2fastx
-rwxr-xr-x root/root 139136 2018-08-18 07:28 ./usr/bin/bam_merge
-rwxr-xr-x root/root 1925 2018-08-18 07:28 ./usr/bin/bed_to_juncs
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-rwxr-xr-x root/root 159616 2018-08-18 07:28 ./usr/bin/map2gtf
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-rwxr-xr-x root/root 229248 2018-08-18 07:28 ./usr/bin/sam_juncs
-rwxr-xr-x root/root 438412 2018-08-18 07:28 ./usr/bin/segment_juncs
-rwxr-xr-x root/root 716 2018-08-18 07:28 ./usr/bin/sra_to_solid
-rwxr-xr-x root/root 171670 2018-08-18 07:28 ./usr/bin/tophat
-rwxr-xr-x root/root 118409 2018-08-18 07:28 ./usr/bin/tophat-fusion-post
-rwxr-xr-x root/root 166 2018-08-18 07:28 ./usr/bin/tophat2
-rwxr-xr-x root/root 438144 2018-08-18 07:28 ./usr/bin/tophat_reports
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drwxr-xr-x root/root 0 2018-08-18 07:28 ./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 2018-08-18 07:28 ./usr/share/doc/tophat/README.test
-rw-r--r-- root/root 3314 2018-08-18 07:28 ./usr/share/doc/tophat/changelog.Debian.gz
-rw-r--r-- root/root 2723 2018-08-18 07:28 ./usr/share/doc/tophat/copyright
-rw-r--r-- root/root 266 2018-08-18 07:28 ./usr/share/doc/tophat/run-unit-test
drwxr-xr-x root/root 0 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/
-rw-r--r-- root/root 1870 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/reads_1.fq.gz
-rw-r--r-- root/root 1863 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/reads_2.fq.gz
-rw-r--r-- root/root 5283 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.1.bt2.gz
-rw-r--r-- root/root 5274 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.1.ebwt.gz
-rw-r--r-- root/root 168 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.2.bt2
-rw-r--r-- root/root 88 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.2.ebwt
-rw-r--r-- root/root 17 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.3.bt2
-rw-r--r-- root/root 163 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.4.bt2
-rw-r--r-- root/root 680 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.fa
-rw-r--r-- root/root 5285 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.rev.1.bt2.gz
-rw-r--r-- root/root 5268 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.rev.1.ebwt.gz
-rw-r--r-- root/root 168 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.rev.2.bt2
-rw-r--r-- root/root 88 2018-08-18 07:28 ./usr/share/doc/tophat/test_data/test_ref.rev.2.ebwt
drwxr-xr-x root/root 0 2018-08-18 07:28 ./usr/share/man/
drwxr-xr-x root/root 0 2018-08-18 07:28 ./usr/share/man/man1/
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-rw-r--r-- root/root 353 2018-08-18 07:28 ./usr/share/man/man1/contig_to_chr_coords.1.gz
-rw-r--r-- root/root 1911 2018-08-18 07:28 ./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: 123132
Build-Time: 1181
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 596
Job: tophat_2.1.1+dfsg1-2
Machine Architecture: armhf
Package: tophat
Package-Time: 1825
Source-Version: 2.1.1+dfsg1-2
Space: 123132
Status: successful
Version: 2.1.1+dfsg1-2
--------------------------------------------------------------------------------
Finished at 2018-08-20T06:28:51Z
Build needed 00:30:25, 123132k disc space