pirs →
2.0.2+dfsg-5.1+b1 →
armhf → 2017-04-09 12:16:49
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| pirs 2.0.2+dfsg-5.1+b1 (armhf) Sun, 09 Apr 2017 12:07:52 +0000 |
+==============================================================================+
Package: pirs
Version: 2.0.2+dfsg-5.1+b1
Source Version: 2.0.2+dfsg-5.1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-625c3682-cb92-4838-a64c-2b0a874f9c39' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9733 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 27s (770 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: 'pirs' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/pirs.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/pirs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 6038 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pirs 2.0.2+dfsg-5.1 (dsc) [2132 B]
Get:2 http://172.17.0.1/private stretch-staging/main pirs 2.0.2+dfsg-5.1 (tar) [6029 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pirs 2.0.2+dfsg-5.1 (diff) [6536 B]
Fetched 6038 kB in 1s (3187 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pirs-c8Yqj3/pirs-2.0.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pirs-c8Yqj3' 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-qF4BUt/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-qF4BUt/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-qF4BUt/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-qF4BUt/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (2855 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:
fuse2fs gnupg-l10n kbd libfuse2 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 54 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13261 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 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), dh-autoreconf, libboost-dev, zlib1g-dev, libgzstream-dev
Filtered Build-Depends: debhelper (>= 10), dh-autoreconf, libboost-dev, zlib1g-dev, libgzstream-dev
dpkg-deb: building package 'sbuild-build-depends-pirs-dummy' in '/<<BUILDDIR>>/resolver-qF4BUt/apt_archive/sbuild-build-depends-pirs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pirs-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-qF4BUt/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ Sources [522 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ Packages [601 B]
Fetched 2456 B in 0s (3327 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pirs 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:
fuse2fs gnupg-l10n kbd libfuse2 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libboost-dev libboost1.62-dev libbsd0
libcroco3 libffi6 libfile-stripnondeterminism-perl libglib2.0-0
libgzstream-dev libgzstream0 libicu57 libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libboost-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libboost-dev libboost1.62-dev libbsd0
libcroco3 libffi6 libfile-stripnondeterminism-perl libglib2.0-0
libgzstream-dev libgzstream0 libicu57 libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
po-debconf sbuild-build-depends-pirs-dummy zlib1g-dev
0 upgraded, 37 newly installed, 0 to remove and 54 not upgraded.
Need to get 26.4 MB/26.4 MB of archives.
After this operation, 182 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-qF4BUt/apt_archive ./ sbuild-build-depends-pirs-dummy 0.invalid.0 [806 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-3 [221 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-3 [104 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-3 [63.2 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.2 [806 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.032-1 [15.8 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.032-1 [9888 B]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.3-2 [2527 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.62.0.1+b4 [3920 B]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libgzstream0 armhf 1.5+dfsg-2 [5764 B]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libgzstream-dev armhf 1.5+dfsg-2 [6172 B]
Get:36 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package groff-base.
(Reading database ... 13261 files and directories currently installed.)
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Unpacking groff-base (1.22.3-9) ...
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Preparing to unpack .../04-man-db_2.7.6.1-2_armhf.deb ...
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Setting up libarchive-zip-perl (1.59-1) ...
Setting up libgzstream0 (1.5+dfsg-2) ...
Setting up libboost1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up libgzstream-dev (1.5+dfsg-2) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-9) ...
Setting up gettext-base (0.19.8.1-2) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-5) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.2) ...
Setting up libmagic-mgc (1:5.29-3) ...
Setting up libmagic1:armhf (1:5.29-3) ...
Processing triggers for libc-bin (2.24-9) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up libboost-dev:armhf (1.62.0.1+b4) ...
Setting up bsdmainutils (9.0.12) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up autopoint (0.19.8.1-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.032-1) ...
Setting up libglib2.0-0:armhf (2.50.3-2) ...
No schema files found: doing nothing.
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-3) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up gettext (0.19.8.1-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.032-1) ...
Setting up debhelper (10.2.5) ...
Setting up sbuild-build-depends-pirs-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-9) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.90.20170124-2 dpkg-dev_1.18.22 g++-6_6.3.0-6+rpi1 gcc-6_6.3.0-6+rpi1 libc6-dev_2.24-9 libstdc++-6-dev_6.3.0-6+rpi1 libstdc++6_6.3.0-6+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4~rc1 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.8+rpi1 base-passwd_3.5.43 bash_4.4-4 binutils_2.27.90.20170124-2 bsdmainutils_9.0.12 bsdutils_1:2.29.1-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-2 cpio_2.11+dfsg-6 cpp_4:6.3.0-1 cpp-6_6.3.0-6+rpi1 dash_0.5.8-2.4 debconf_1.5.60 debfoster_2.7-2.1 debhelper_10.2.5 debianutils_4.8.1 dh-autoreconf_14 dh-strip-nondeterminism_0.032-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-1 dpkg_1.18.22 dpkg-dev_1.18.22 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.29-3 findutils_4.6.0+git+20161106-2 fuse2fs_1.43.4-2 g++_4:6.3.0-1 g++-6_6.3.0-6+rpi1 gcc_4:6.3.0-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.3.0-6+rpi1 gcc-6-base_6.3.0-6+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gnupg_2.1.18-3 gnupg-agent_2.1.18-3 gnupg-l10n_2.1.18-3 gpgv_2.1.18-3 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.9 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libapparmor1_2.11.0-2 libapt-pkg5.0_1.4~rc1 libarchive-zip-perl_1.59-1 libasan3_6.3.0-6+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29.1-1 libboost-dev_1.62.0.1+b4 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9 libc-dev-bin_2.24-9 libc6_2.24-9 libc6-dev_2.24-9 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.3.0-6+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-3 libdb5.3_5.3.28-12 libdbus-1-3_1.10.16-1 libdebconfclient0_0.220 libdevmapper1.02.1_2:1.02.137-1 libdpkg-perl_1.18.22 libdrm2_2.4.74-1 libfakeroot_1.21-3.1 libfdisk1_2.29.1-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.032-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.3.0-6+rpi1 libgcc1_1:6.3.0-6+rpi1 libgcrypt20_1.7.6-1 libgdbm3_1.8.3-14 libglib2.0-0_2.50.3-2 libgmp10_2:6.1.2+dfsg-1 libgomp1_6.3.0-6+rpi1 libgpg-error0_1.26-2 libgzstream-dev_1.5+dfsg-2 libgzstream0_1.5+dfsg-2 libicu57_57.1-5 libidn11_1.33-1 libip4tc0_1.6.0+snapshot20161117-5 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_23-2 libksba8_1.3.5-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-3 libmagic1_1:5.29-3 libmount1_2.29.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnpth0_1.3-1 libpam-modules_1.1.8-3.5 libpam-modules-bin_1.1.8-3.5 libpam-runtime_1.1.8-3.5 libpam0g_1.1.8-3.5 libpcre3_2:8.39-2 libperl5.24_5.24.1-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-3 libreadline7_7.0-2 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libsmartcols1_2.29.1-1 libsqlite3-0_3.16.2-2 libss2_1.43.4-2 libstdc++-6-dev_6.3.0-6+rpi1 libstdc++6_6.3.0-6+rpi1 libsystemd0_232-18 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libubsan0_6.3.0-6+rpi1 libudev1_232-18 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29.1-1 libxml2_2.9.4+dfsg1-2.2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-3 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.09-2 mawk_1.3.3-17 mount_2.29.1-1 multiarch-support_2.24-9 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 netbase_5.4 passwd_1:4.4-3 patch_2.7.5-1 perl_5.24.1-1 perl-base_5.24.1-1 perl-modules-5.24_5.24.1-1 pinentry-curses_1.0.0-2 po-debconf_1.0.20 procps_2:3.3.12-3 psmisc_22.21-2.1 raspbian-archive-keyring_20120528.2 readline-common_7.0-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pirs-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-18 systemd-sysv_232-18 sysv-rc_2.88dsf-59.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2016j-2 udev_232-18 util-linux_2.29.1-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Jan 14 16:31:17 2017 UTC
gpgv: using RSA key 62FF8A7584E029569546000674263B37F5B5F913
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pirs_2.0.2+dfsg-5.1.dsc
dpkg-source: info: extracting pirs in /<<BUILDDIR>>/pirs-2.0.2+dfsg
dpkg-source: info: unpacking pirs_2.0.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking pirs_2.0.2+dfsg-5.1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_libgzstream.patch
dpkg-source: info: applying Fix-spelling-of-sse2-option.patch
dpkg-source: info: applying do_not_seek_for_arial.ttf.patch
dpkg-source: info: applying Remove-mtune-compiler-flag.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.0.2+dfsg-5.1+b1
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=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-625c3682-cb92-4838-a64c-2b0a874f9c39
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pirs
dpkg-buildpackage: info: source version 2.0.2+dfsg-5.1+b1
dpkg-buildpackage: info: source distribution stretch-staging
dpkg-source --before-build pirs-2.0.2+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf --sourcedirectory=src
dh_testdir -O--sourcedirectory=src
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_auto_clean
cd src && ./srclean.sh >/dev/null 2>/dev/null || true
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_autoreconf_clean -O--sourcedirectory=src
dh_clean -O--sourcedirectory=src
debian/rules build-arch
dh build-arch --with autoreconf --sourcedirectory=src
dh_testdir -a -O--sourcedirectory=src
dh_update_autotools_config -a -O--sourcedirectory=src
debian/rules override_dh_autoreconf
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
#cd src && ./genauto.sh
cd src && \
mv INSTALL INSTALL.save && \
autoreconf --install && \
mv INSTALL.save INSTALL && \
cd /<<BUILDDIR>>/pirs-2.0.2+dfsg
configure.ac:9: installing './compile'
configure.ac:3: installing './install-sh'
configure.ac:3: installing './missing'
Makefile.am: installing './INSTALL'
pirs/Makefile.am:28: warning: source file 'SFMT-src-1.4/SFMT.c' is in a subdirectory,
pirs/Makefile.am:28: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
pirs/Makefile.am: installing './depcomp'
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_auto_configure -- --enable-pirs-diploid --disable-sse2
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --enable-pirs-diploid --disable-sse2
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for gzopen in -lz... yes
checking Whether to include support for 'pirs diploid' command... yes
checking Whether to include support for 'pirs simulate' command... yes
checking Whether to include support for multiple threads... yes
checking for g++ option to support OpenMP... -fopenmp
checking Whether to include support for SSE2 instructions... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating pirs/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_auto_build
make -j4
make[2]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /<<BUILDDIR>>/pirs-2.0.2+dfsg/src/missing autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make all-recursive
make[3]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
Making all in pirs
make[4]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src/pirs'
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o InputStream.o InputStream.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputStream.o OutputStream.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o util.o util.cpp
main.cpp:18:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
"Compile Date: " __DATE__ " time: " __TIME__ "\n"
^~~~~~~~
main.cpp:18:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
"Compile Date: " __DATE__ " time: " __TIME__ "\n"
^~~~~~~~
util.cpp: In function 'void* xmalloc(size_t)':
util.cpp:192:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t {aka unsigned int}' [-Wformat=]
fatal_error("Out of memory: tried to allocate %lu bytes", size);
^
util.cpp: In function 'void* xrealloc(void*, size_t)':
util.cpp:200:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t {aka unsigned int}' [-Wformat=]
fatal_error("Out of memory: tried to reallocate %lu bytes", size);
^
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o mt19937-64.o mt19937-64.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_diploid.o pirs_diploid.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o BaseCallingProfile.o BaseCallingProfile.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.cpp
pirs_diploid.cpp:639:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
^
pirs_diploid.cpp:639:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
^
pirs_diploid.cpp:639:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
^
pirs_diploid.cpp:641:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
^
pirs_diploid.cpp:641:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
^
pirs_diploid.cpp:641:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
^
pirs_diploid.cpp:643:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info(" %#"PRIx64"]\n", het_type_tab[6]);
^
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp
pirs_diploid.cpp: In function 'bool try_indel(const double*, const size_t*, const std::vector<char>&, size_t&, std::vector<char>&, bool, const char*, Counter&)':
pirs_diploid.cpp:438:20: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
indel_len);
^
pirs_diploid.cpp:438:20: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
IndelProfile.cpp: In function 'void load_indel_info_line(char*, Profile&)':
IndelProfile.cpp:117:50: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t* {aka long long unsigned int*}' [-Wformat=]
} else if (sscanf(line, "Read_1_Count = %lu", &n) == 1)
^
IndelProfile.cpp:119:48: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t* {aka long long unsigned int*}' [-Wformat=]
else if (sscanf(line, "Read_2_Count = %lu", &n) == 1)
^
IndelProfile.cpp: In constructor 'IndelProfile::IndelProfile(const SimulationParameters&)':
IndelProfile.cpp:165:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
info(" read_1_count = %lu\n", read_1_count);
^
IndelProfile.cpp:166:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
info(" read_2_count = %lu\n", read_2_count);
^
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskQvalsByEamss.o MaskQvalsByEamss.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o Profile.o Profile.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp
pirs_simulate.cpp:168:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
" "DEFAULT_BASE_CALLING_PROFILE"\n"
^
pirs_simulate.cpp:174:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
" "DEFAULT_INDEL_PROFILE"\n"
^
pirs_simulate.cpp:180:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
" "DEFAULT_GC_BIAS_PROFILE_100",\n"
^
pirs_simulate.cpp:181:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
" "DEFAULT_GC_BIAS_PROFILE_150",\n"
^
pirs_simulate.cpp:182:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
" "DEFAULT_GC_BIAS_PROFILE_200",\n"
^
pirs_simulate.cpp:672:18: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
out_file.printf("%cread_%d_%"PRIu64"/%d\n",
^
pirs_simulate.cpp:700:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info_log_file.printf("read_%d_%"PRIu64"/%d\t%s\t%s\t%zu\t%c\t%d\t%d\t",
^
pirs_simulate.cpp:1235:10: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Simulated %"PRIu64" of %"PRIu64" read pairs\n",
^
pirs_simulate.cpp:1235:29: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Simulated %"PRIu64" of %"PRIu64" read pairs\n",
^
pirs_simulate.cpp:1540:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
insert_log.printf("%d\t%"PRIu64"\n", it->first, it->second);
^
pirs_simulate.cpp:1557:2: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
"# The total number of read pairs that were simulated was %"PRIu64".\n"
^
pirs_simulate.cpp:1574:20: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
error_log.printf("%d\t%"PRIu64"\t%g\n",
^
pirs_simulate.cpp:1579:19: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
error_log.printf("total\t%"PRIu64"\t%g\n",
^
pirs_simulate.cpp:1685:26: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
log_parameter(info_log, "Random seed: %"PRIu64"\n",
^
pirs_simulate.cpp:1713:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Program: "PROGRAM "\n");
^
pirs_simulate.cpp:1714:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Version: "VERSION "\n");
^
pirs_simulate.cpp:1715:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Author: "AUTHOR "\n");
^
pirs_simulate.cpp:1716:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Contact: "CONTACT "\n");
^
pirs_simulate.cpp:1717:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Compile Date: "__DATE__ " time: " __TIME__ "\n");
^
pirs_simulate.cpp:1717:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
info("Compile Date: "__DATE__ " time: " __TIME__ "\n");
^~~~~~~~
pirs_simulate.cpp:1717:44: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
info("Compile Date: "__DATE__ " time: " __TIME__ "\n");
^~~~~~~~
pirs_simulate.cpp:1764:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Bases in reference sequences: %"PRIu64"\n",
^
pirs_simulate.cpp:1766:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Read pairs simulated: %"PRIu64"\n",
^
pirs_simulate.cpp:1768:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Bases in reads: %"PRIu64"\n",
^
pirs_simulate.cpp:1773:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Substitution error count: %"PRIu64"\n",
^
pirs_simulate.cpp:1777:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Insertion count: %"PRIu64"\n",
^
pirs_simulate.cpp:1779:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Deletion count: %"PRIu64"\n",
^
pirs_simulate.cpp:1795:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Bases masked by EAMSS algorithm: %"PRIu64"\n", counters.masked_bases);
^
pirs_simulate.cpp:1856:8: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
info("Note: A random seed (%"PRIu64") was specified on the command line.\n",
^
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pirs-2.0.2+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now -o pirs InputStream.o OutputStream.o main.o util.o mt19937-64.o pirs_diploid.o BaseCallingProfile.o GCBiasProfile.o IndelProfile.o MaskQvalsByEamss.o Profile.o pirs_simulate.o -lz -lz
make[4]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src/pirs'
make[4]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
cd src/stator/gcContCvgBias && make
make[2]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src/stator/gcContCvgBias'
g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal self_util.cpp self_util.h
g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal main.cpp
g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal stat_soap_coverage.h stat_soap_coverage.cpp
g++ -o gc_coverage_bias -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal self_util.o main.o stat_soap_coverage.o -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now -lgzstream -lz
make[2]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src/stator/gcContCvgBias'
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_auto_test -a -O--sourcedirectory=src
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
Making check in pirs
make[2]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src/pirs'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src/pirs'
make[2]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg/src'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf --sourcedirectory=src
dh_testroot -a -O--sourcedirectory=src
dh_prep -a -O--sourcedirectory=src
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_auto_install --sourcedirectory=src/stator/gcContCvgBias
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_install
mkdir -p debian/pirs/usr/lib/pirs
find src -name "*.pl" -exec cp -a \{\} debian/pirs/usr/lib/pirs \;
rm -f debian/pirs/usr/lib/pirs/autobam.pl
sed -i 's:#!/bin/env:#!/usr/bin/env:' debian/pirs/usr/lib/pirs/*.pl
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
debian/rules override_dh_installdocs-arch
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_installdocs -a
cp -a src/stator/readme.txt debian/pirs/usr/share/doc/pirs/strator_readme.txt
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_installchangelogs NEWS
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_perl -a -O--sourcedirectory=src
debian/rules override_dh_link-arch
make[1]: Entering directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_link -a
for pl in debian/pirs/usr/lib/pirs/*.pl ; do \
plname=`basename ${pl}` ; \
ln -s ../lib/pirs/${plname} debian/pirs/usr/bin/`basename ${plname} .pl` ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/pirs-2.0.2+dfsg'
dh_strip_nondeterminism -a -O--sourcedirectory=src
dh_compress -a -O--sourcedirectory=src
dh_fixperms -a -O--sourcedirectory=src
dh_strip -a -O--sourcedirectory=src
dh_makeshlibs -a -O--sourcedirectory=src
dh_shlibdeps -a -O--sourcedirectory=src
dpkg-shlibdeps: warning: debian/pirs/usr/bin/gc_coverage_bias contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile
dpkg-shlibdeps: warning: debian/pirs/usr/bin/pirs 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/pirs/usr/bin/pirs was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a -O--sourcedirectory=src
dh_gencontrol -a -O--sourcedirectory=src
dpkg-gencontrol: warning: package pirs: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package pirs: unused substitution variable ${perl:Depends}
dh_md5sums -a -O--sourcedirectory=src
dh_builddeb -a -O--sourcedirectory=src
dpkg-deb: building package 'pirs-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-5.1+b1_armhf.deb'.
dpkg-deb: building package 'pirs' in '../pirs_2.0.2+dfsg-5.1+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pirs_2.0.2+dfsg-5.1+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pirs-2.0.2+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-04-09T12:16:40Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pirs_2.0.2+dfsg-5.1+b1_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sat, 14 Jan 2017 17:29:49 +0100
Source: pirs (2.0.2+dfsg-5.1)
Binary: pirs pirs-profiles pirs-examples
Binary-Only: yes
Architecture: armhf
Version: 2.0.2+dfsg-5.1+b1
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
pirs - Profile based Illumina pair-end Reads Simulator
pirs-examples - profile basd Illumina pair-end Reads Simulator (example data)
pirs-profiles - profile basd Illumina pair-end Reads Simulator (profile data)
Changes:
pirs (2.0.2+dfsg-5.1+b1) stretch-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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5f8689af5d93408a269c07f8ae73c75d5b9eeb0f 97594 pirs_2.0.2+dfsg-5.1+b1_armhf.deb
857f60c6bce6650a32f37b66265d3caba38e2095 4931 pirs_2.0.2+dfsg-5.1_armhf.buildinfo
Checksums-Sha256:
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72a2164c5884a3ee1e1a493ba2a1d7b15faa23ebc946b2eefba91d2fdb39e990 97594 pirs_2.0.2+dfsg-5.1+b1_armhf.deb
a1974c669cee3d372de2b1d41a8373a26835c39ee07716d630da10b8fd2f5939 4931 pirs_2.0.2+dfsg-5.1_armhf.buildinfo
Files:
cf78d10e158fbf16c650f5ef08ab1042 310788 debug extra pirs-dbgsym_2.0.2+dfsg-5.1+b1_armhf.deb
e2b2dff3a63feeaef4bf10bf563b44d2 97594 science optional pirs_2.0.2+dfsg-5.1+b1_armhf.deb
068f008dde998e6897d20a597835415f 4931 science optional pirs_2.0.2+dfsg-5.1_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pirs-dbgsym_2.0.2+dfsg-5.1+b1_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 310788 bytes: control archive=555 bytes.
477 bytes, 13 lines control
212 bytes, 2 lines md5sums
Package: pirs-dbgsym
Source: pirs (2.0.2+dfsg-5.1)
Version: 2.0.2+dfsg-5.1+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 356
Depends: pirs (= 2.0.2+dfsg-5.1+b1)
Section: debug
Priority: extra
Homepage: https://github.com/galaxy001/pirs
Description: Debug symbols for pirs
Build-Ids: b70edf7189c7d3c6e843c73573e8a54a461b0400 e95add084b4a9a3be9c9e076075bcfeeb6721d86
drwxr-xr-x root/root 0 2017-01-14 16:29 ./
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/lib/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/lib/debug/.build-id/b7/
-rw-r--r-- root/root 325536 2017-01-14 16:29 ./usr/lib/debug/.build-id/b7/0edf7189c7d3c6e843c73573e8a54a461b0400.debug
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/lib/debug/.build-id/e9/
-rw-r--r-- root/root 27644 2017-01-14 16:29 ./usr/lib/debug/.build-id/e9/5add084b4a9a3be9c9e076075bcfeeb6721d86.debug
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/share/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/share/doc/pirs-dbgsym -> pirs
pirs_2.0.2+dfsg-5.1+b1_armhf.deb
--------------------------------
new debian package, version 2.0.
size 97594 bytes: control archive=1673 bytes.
1412 bytes, 28 lines control
1607 bytes, 24 lines md5sums
Package: pirs
Source: pirs (2.0.2+dfsg-5.1)
Version: 2.0.2+dfsg-5.1+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 322
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libgzstream0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.0.2), pirs-profiles, ttf-liberation, gnuplot
Section: science
Priority: optional
Homepage: https://github.com/galaxy001/pirs
Description: Profile based Illumina pair-end Reads Simulator
The program pIRS can be used for simulating Illumina PE reads, with a
series of characters generated by Illumina sequencing platform, such as
insert size distribution, sequencing error(substitution, insertion,
deletion), quality score and GC content-coverage bias.
.
The insert size follows a normal distribution, so users should set the
mean value and standard deviation. Usually the standard deviation is set
as 1/20 of the mean value. The normal distribution by Box-Muller method
is simulated.
.
The program simulates sequencing error, quality score and GC content-
coverage bias according to the empirical distribution profile. Some
default profiles counted from lots of real sequencing data are provided.
.
To simulate reads from diploid genome, users should simulate the diploid
genome sequence firstly by setting the ratio of heterozygosis SNP,
heterozygosis InDel and structure variation.
drwxr-xr-x root/root 0 2017-01-14 16:29 ./
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/bin/
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/alignment_stator -> ../lib/pirs/alignment_stator.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/baseCalling_Matrix_analyzer -> ../lib/pirs/baseCalling_Matrix_analyzer.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/baseCalling_Matrix_calculator -> ../lib/pirs/baseCalling_Matrix_calculator.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/baseCalling_Matrix_calculator.0 -> ../lib/pirs/baseCalling_Matrix_calculator.0.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/baseCalling_Matrix_merger -> ../lib/pirs/baseCalling_Matrix_merger.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/baseCalling_Matrix_merger.old -> ../lib/pirs/baseCalling_Matrix_merger.old.pl
-rwxr-xr-x root/root 79552 2017-01-14 16:29 ./usr/bin/gc_coverage_bias
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/gc_coverage_bias_plot -> ../lib/pirs/gc_coverage_bias_plot.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/gethist -> ../lib/pirs/gethist.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/ifollowQ -> ../lib/pirs/ifollowQ.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/ifollowQmerge -> ../lib/pirs/ifollowQmerge.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/ifollowQplot -> ../lib/pirs/ifollowQplot.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/ifqQ -> ../lib/pirs/ifqQ.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/indelstat_sam_bam -> ../lib/pirs/indelstat_sam_bam.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/itilestator -> ../lib/pirs/itilestator.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/loess -> ../lib/pirs/loess.pl
lrwxrwxrwx root/root 0 2017-01-14 16:29 ./usr/bin/pifollowQmerge -> ../lib/pirs/pifollowQmerge.pl
-rwxr-xr-x root/root 87644 2017-01-14 16:29 ./usr/bin/pirs
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/lib/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/lib/pirs/
-rwxr-xr-x root/root 15718 2017-01-14 16:29 ./usr/lib/pirs/alignment_stator.pl
-rwxr-xr-x root/root 11248 2017-01-14 16:29 ./usr/lib/pirs/baseCalling_Matrix_analyzer.pl
-rwxr-xr-x root/root 20939 2017-01-14 16:29 ./usr/lib/pirs/baseCalling_Matrix_calculator.0.pl
-rwxr-xr-x root/root 19568 2017-01-14 16:29 ./usr/lib/pirs/baseCalling_Matrix_calculator.pl
-rwxr-xr-x root/root 5676 2017-01-14 16:29 ./usr/lib/pirs/baseCalling_Matrix_merger.old.pl
-rwxr-xr-x root/root 6284 2017-01-14 16:29 ./usr/lib/pirs/baseCalling_Matrix_merger.pl
-rwxr-xr-x root/root 3235 2017-01-14 16:29 ./usr/lib/pirs/gc_coverage_bias_plot.pl
-rwxr-xr-x root/root 362 2017-01-14 16:29 ./usr/lib/pirs/gethist.pl
-rwxr-xr-x root/root 4059 2017-01-14 16:29 ./usr/lib/pirs/ifollowQ.pl
-rwxr-xr-x root/root 3534 2017-01-14 16:29 ./usr/lib/pirs/ifollowQmerge.pl
-rwxr-xr-x root/root 617 2017-01-14 16:29 ./usr/lib/pirs/ifollowQplot.pl
-rw-r--r-- root/root 1824 2017-01-14 16:29 ./usr/lib/pirs/ifqQ.pl
-rwxr-xr-x root/root 7232 2017-01-14 16:29 ./usr/lib/pirs/indelstat_sam_bam.pl
-rwxr-xr-x root/root 2683 2017-01-14 16:29 ./usr/lib/pirs/itilestator.pl
-rw-r--r-- root/root 1460 2017-01-14 16:29 ./usr/lib/pirs/loess.pl
-rwxr-xr-x root/root 3084 2017-01-14 16:29 ./usr/lib/pirs/pifollowQmerge.pl
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/share/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-01-14 16:29 ./usr/share/doc/pirs/
-rw-r--r-- root/root 7184 2016-08-14 05:10 ./usr/share/doc/pirs/README.gz
-rw-r--r-- root/root 225 2017-01-14 16:29 ./usr/share/doc/pirs/changelog.Debian.armhf.gz
-rw-r--r-- root/root 651 2017-01-14 16:29 ./usr/share/doc/pirs/changelog.Debian.gz
-rw-r--r-- root/root 3446 2016-08-14 05:10 ./usr/share/doc/pirs/changelog.gz
-rw-r--r-- root/root 2931 2017-01-14 08:44 ./usr/share/doc/pirs/copyright
-rw-r--r-- root/root 1288 2016-08-14 05:10 ./usr/share/doc/pirs/strator_readme.txt
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 42296
Build-Time: 171
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 304
Job: pirs_2.0.2+dfsg-5.1
Machine Architecture: armhf
Package: pirs
Package-Time: 528
Source-Version: 2.0.2+dfsg-5.1
Space: 42296
Status: successful
Version: 2.0.2+dfsg-5.1+b1
--------------------------------------------------------------------------------
Finished at 2017-04-09T12:16:40Z
Build needed 00:08:48, 42296k disc space