Sun Feb 23 23:25:58 UTC 2025 I: starting to build pirs/trixie/i386 on jenkins on '2025-02-23 23:25'
Sun Feb 23 23:25:58 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_1/57631/console.log
Sun Feb 23 23:25:58 UTC 2025 I: Downloading source for trixie/pirs=2.0.2+dfsg-12
--2025-02-23 23:25:58-- http://deb.debian.org/debian/pool/main/p/pirs/pirs_2.0.2%2bdfsg-12.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2123 (2.1K) [text/prs.lines.tag]
Saving to: ‘pirs_2.0.2+dfsg-12.dsc’
0K .. 100% 347M=0s
2025-02-23 23:25:58 (347 MB/s) - ‘pirs_2.0.2+dfsg-12.dsc’ saved [2123/2123]
Sun Feb 23 23:25:58 UTC 2025 I: pirs_2.0.2+dfsg-12.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: pirs
Binary: pirs, pirs-profiles, pirs-examples
Architecture: any all
Version: 2.0.2+dfsg-12
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/galaxy001/pirs
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/pirs
Vcs-Git: https://salsa.debian.org/med-team/pirs.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libboost-dev, zlib1g-dev, libgzstream-dev
Package-List:
pirs deb science optional arch=any
pirs-examples deb science optional arch=all
pirs-profiles deb science optional arch=all
Checksums-Sha1:
f7ad7b1afb04ddb941cf2aa00a368ee61883fcdd 6029204 pirs_2.0.2+dfsg.orig.tar.xz
8fbede7a6e6614848e23962eb89cf3f547400ed7 8148 pirs_2.0.2+dfsg-12.debian.tar.xz
Checksums-Sha256:
ef7ed1400dafd06f29a699023f0ecdcd52e0073254c87646c4ecea803e4b1d93 6029204 pirs_2.0.2+dfsg.orig.tar.xz
f11d153d48e2830a72586a92afc6c21f9a51136ca800590055d3fde53aeb45d0 8148 pirs_2.0.2+dfsg-12.debian.tar.xz
Files:
1ee1373ad8b358f61adc8429645f946d 6029204 pirs_2.0.2+dfsg.orig.tar.xz
09e4b580bb20a62ce8f71af98b38815a 8148 pirs_2.0.2+dfsg-12.debian.tar.xz
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Sun Feb 23 23:25:58 UTC 2025 I: Checking whether the package is not for us
Sun Feb 23 23:25:58 UTC 2025 I: Starting 1st build on remote node ionos2-i386.debian.net.
Sun Feb 23 23:25:58 UTC 2025 I: Preparing to do remote build '1' on ionos2-i386.debian.net.
Sun Feb 23 23:27:16 UTC 2025 I: Deleting $TMPDIR on ionos2-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Feb 23 11:26:00 -12 2025
I: pbuilder-time-stamp: 1740353160
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [pirs_2.0.2+dfsg-12.dsc]
I: copying [./pirs_2.0.2+dfsg.orig.tar.xz]
I: copying [./pirs_2.0.2+dfsg-12.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./pirs_2.0.2+dfsg-12.dsc: unsupported subcommand
dpkg-source: info: extracting pirs in 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-12.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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
dpkg-source: info: applying gcc-12.patch
dpkg-source: info: applying typos.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/56832/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='ab0fceb01d8044359e7011e03dfb3957'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='56832'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.7kzKPa5G/pbuilderrc_KQi9 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7kzKPa5G/b1 --logfile b1/build.log pirs_2.0.2+dfsg-12.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://46.16.76.132:3128'
I: uname -a
Linux ionos2-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/56832/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), libboost-dev, zlib1g-dev, libgzstream-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19791 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on libboost-dev; however:
Package libboost-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgzstream-dev; however:
Package libgzstream-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgzstream-dev{a} libgzstream0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded.
Need to get 32.3 MB of archives. After unpacking 241 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-3 [96.2 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-4.1 [10.6 MB]
Get: 32 http://deb.debian.org/debian trixie/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B]
Get: 33 http://deb.debian.org/debian trixie/main i386 libgzstream0 i386 1.5+git20171107.9a20658-3 [7192 B]
Get: 34 http://deb.debian.org/debian trixie/main i386 libgzstream-dev i386 1.5+git20171107.9a20658-3 [7568 B]
Get: 35 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 32.3 MB in 1s (57.3 MB/s)
Preconfiguring packages ...
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(Reading database ... 19791 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
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Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
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Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ...
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Preparing to unpack .../04-gettext-base_0.23.1-1_i386.deb ...
Unpacking gettext-base (0.23.1-1) ...
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Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
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Preparing to unpack .../06-groff-base_1.23.0-7_i386.deb ...
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Setting up libpipeline1:i386 (1.5.8-1) ...
Setting up libboost1.83-dev:i386 (1.83.0-4.1) ...
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Setting up bsdextrautils (2.40.4-3) ...
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Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:i386 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up libgzstream0:i386 (1.5+git20171107.9a20658-3) ...
Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libboost-dev:i386 (1.83.0.2+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libgzstream-dev:i386 (1.5+git20171107.9a20658-3) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/pirs-2.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pirs_2.0.2+dfsg-12_source.changes
dpkg-buildpackage: info: source package pirs
dpkg-buildpackage: info: source version 2.0.2+dfsg-12
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --sourcedirectory=src
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_auto_clean
cd src && ./srclean.sh >/dev/null 2>/dev/null || true
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_autoreconf_clean -O--sourcedirectory=src
dh_clean -O--sourcedirectory=src
debian/rules binary
dh binary --sourcedirectory=src
dh_update_autotools_config -O--sourcedirectory=src
debian/rules override_dh_autoreconf
make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg'
cd src && \
mv INSTALL INSTALL.save && \
autoreconf --install && \
mv INSTALL.save INSTALL && \
cd /build/reproducible-path/pirs-2.0.2+dfsg
configure.ac:5: warning: The macro 'AC_CONFIG_HEADER' is obsolete.
configure.ac:5: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:5: the top level
configure.ac:71: warning: AC_OUTPUT should be used without arguments.
configure.ac:71: You should run autoupdate.
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 one 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, this
automake: behavior may change in a future Automake major version, with object
automake: files being placed in the same subdirectory as the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibility.
pirs/Makefile.am: installing './depcomp'
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_auto_configure -- --enable-pirs-diploid --disable-sse2
cd src && ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-pirs-diploid --disable-sse2
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/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 xargs -n works... 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 the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... 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
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_auto_build
cd src && make -j11
make[2]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
make all-recursive
make[3]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
Making all in pirs
make[4]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src/pirs'
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -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 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -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 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -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 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.o util.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -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 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -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 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -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 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -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 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -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 -DBOOST_TIMER_ENABLE_DEPRECATED -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp
main.cpp:18:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n"
| ^~~~~~~~
main.cpp:18:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n"
| ^~~~~~~~
pirs_diploid.cpp:640:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
640 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
| ^
pirs_diploid.cpp:640:28: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
640 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
| ^
pirs_diploid.cpp:640:40: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
640 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
| ^
pirs_diploid.cpp:642:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
| ^
pirs_diploid.cpp:642:28: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
| ^
pirs_diploid.cpp:642:40: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
642 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
| ^
pirs_diploid.cpp:644:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
644 | info(" %#"PRIx64"]\n", het_type_tab[6]);
| ^
pirs_simulate.cpp:168:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
168 | " "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]
174 | " "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]
180 | " "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]
181 | " "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]
182 | " "DEFAULT_GC_BIAS_PROFILE_200",\n"
| ^
pirs_simulate.cpp:672:25: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
672 | out_file.printf("%cread_%d_%"PRIu64"/%d\n",
| ^
pirs_simulate.cpp:700:30: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
700 | info_log_file.printf("read_%d_%"PRIu64"/%d\t%s\t%s\t%zu\t%c\t%d\t%d\t",
| ^
pirs_simulate.cpp:1235:38: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n",
| ^
pirs_simulate.cpp:1235:57: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n",
| ^
pirs_simulate.cpp:1540:35: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1540 | insert_log.printf("%d\t%"PRIu64"\n", it->first, it->second);
| ^
pirs_simulate.cpp:1557:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1557 | "# The total number of read pairs that were simulated was %"PRIu64".\n"
| ^
pirs_simulate.cpp:1574:34: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1574 | error_log.printf("%d\t%"PRIu64"\t%g\n",
| ^
pirs_simulate.cpp:1579:26: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1579 | error_log.printf("total\t%"PRIu64"\t%g\n",
| ^
pirs_simulate.cpp:1685:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1685 | log_parameter(info_log, "Random seed: %"PRIu64"\n",
| ^
pirs_simulate.cpp:1713:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1713 | info("Program: "PROGRAM "\n");
| ^
pirs_simulate.cpp:1714:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1714 | info("Version: "VERSION "\n");
| ^
pirs_simulate.cpp:1715:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1715 | info("Author: "AUTHOR "\n");
| ^
pirs_simulate.cpp:1716:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1716 | info("Contact: "CONTACT "\n");
| ^
pirs_simulate.cpp:1717:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n");
| ^
pirs_simulate.cpp:1717:32: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n");
| ^~~~~~~~
pirs_simulate.cpp:1717:51: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n");
| ^~~~~~~~
pirs_simulate.cpp:1764:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1764 | info("Bases in reference sequences: %"PRIu64"\n",
| ^
pirs_simulate.cpp:1766:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1766 | info("Read pairs simulated: %"PRIu64"\n",
| ^
In file included from InputStream.cpp:1:
InputStream.h: In constructor 'InputStream::InputStream()':
InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
50 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
InputStream.h: In constructor 'InputStream::InputStream(const char*)':
InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
pirs_simulate.cpp:1768:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1768 | info("Bases in reads: %"PRIu64"\n",
| ^
pirs_simulate.cpp:1773:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1773 | info("Substitution error count: %"PRIu64"\n",
| ^
pirs_simulate.cpp:1777:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1777 | info("Insertion count: %"PRIu64"\n",
| ^
pirs_simulate.cpp:1779:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1779 | info("Deletion count: %"PRIu64"\n",
| ^
pirs_simulate.cpp:1795:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1795 | info("Bases masked by EAMSS algorithm: %"PRIu64"\n", counters.masked_bases);
| ^
pirs_simulate.cpp:1856:22: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
1856 | info("Note: A random seed (%"PRIu64") was specified on the command line.\n",
| ^
In file included from OutputStream.cpp:1:
OutputStream.h: In constructor 'OutputStream::OutputStream()':
OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)':
OutputStream.h:58:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
58 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
In file included from Profile.cpp:2:
InputStream.h: In constructor 'InputStream::InputStream()':
InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
50 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
InputStream.h: In constructor 'InputStream::InputStream(const char*)':
InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
In file included from util.cpp:18:
InputStream.h: In constructor 'InputStream::InputStream()':
InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
50 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
InputStream.h: In constructor 'InputStream::InputStream(const char*)':
InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
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=]
192 | fatal_error("Out of memory: tried to allocate %lu bytes", size);
| ~~^ ~~~~
| | |
| | size_t {aka unsigned int}
| long unsigned int
| %u
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=]
200 | fatal_error("Out of memory: tried to reallocate %lu bytes", size);
| ~~^ ~~~~
| | |
| | size_t {aka unsigned int}
| long unsigned int
| %u
In file included from SimulationParameters.h:6,
from GCBiasProfile.h:5,
from GCBiasProfile.cpp:5:
InputStream.h: In constructor 'InputStream::InputStream()':
InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
50 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
InputStream.h: In constructor 'InputStream::InputStream(const char*)':
InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
In file included from SimulationParameters.h:7:
OutputStream.h: In constructor 'OutputStream::OutputStream()':
OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)':
OutputStream.h:58:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
58 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
In file included from SimulationParameters.h:6,
from BaseCallingProfile.h:7,
from BaseCallingProfile.cpp:5:
InputStream.h: In constructor 'InputStream::InputStream()':
InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
50 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
InputStream.h: In constructor 'InputStream::InputStream(const char*)':
InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
In file included from SimulationParameters.h:7:
OutputStream.h: In constructor 'OutputStream::OutputStream()':
OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)':
OutputStream.h:58:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
58 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
In file included from SimulationParameters.h:6,
from IndelProfile.cpp:2:
InputStream.h: In constructor 'InputStream::InputStream()':
InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
50 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
InputStream.h: In constructor 'InputStream::InputStream(const char*)':
InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
In file included from SimulationParameters.h:7:
OutputStream.h: In constructor 'OutputStream::OutputStream()':
OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)':
OutputStream.h:58:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
58 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
In file included from pirs_diploid.cpp:12:
InputStream.h: In constructor 'InputStream::InputStream()':
InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
50 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
InputStream.h: In constructor 'InputStream::InputStream(const char*)':
InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
In file included from pirs_diploid.cpp:13:
OutputStream.h: In constructor 'OutputStream::OutputStream()':
OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)':
OutputStream.h:58:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
58 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
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:436:46: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
436 | indel_log_file.printf("%s\t%zu\t%zu\t%c\t%zu\t",
| ~~^
| |
| unsigned int
| %llu
437 | id, log_ref_seq_idx, log_diploid_seq_idx,
| ~~~~~~~~~~~~~~~
| |
| uint64_t {aka long long unsigned int}
pirs_diploid.cpp:436:51: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
436 | indel_log_file.printf("%s\t%zu\t%zu\t%c\t%zu\t",
| ~~^
| |
| unsigned int
| %llu
437 | id, log_ref_seq_idx, log_diploid_seq_idx,
| ~~~~~~~~~~~~~~~~~~~
| |
| uint64_t {aka long long unsigned int}
IndelProfile.cpp: In function 'void load_indel_info_line(char*, Profile&)':
IndelProfile.cpp:117:51: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=]
117 | } else if (sscanf(line, "Read_1_Count = %lu", &n) == 1)
| ~~^ ~~
| | |
| | uint64_t* {aka long long unsigned int*}
| long unsigned int*
| %llu
IndelProfile.cpp:119:49: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=]
119 | else if (sscanf(line, "Read_2_Count = %lu", &n) == 1)
| ~~^ ~~
| | |
| | uint64_t* {aka long long unsigned int*}
| long unsigned int*
| %llu
IndelProfile.cpp: In constructor 'IndelProfile::IndelProfile(const SimulationParameters&)':
IndelProfile.cpp:165:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
165 | info(" read_1_count = %lu\n", read_1_count);
| ~~^ ~~~~~~~~~~~~
| | |
| | uint64_t {aka long long unsigned int}
| long unsigned int
| %llu
IndelProfile.cpp:166:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
166 | info(" read_2_count = %lu\n", read_2_count);
| ~~^ ~~~~~~~~~~~~
| | |
| | uint64_t {aka long long unsigned int}
| long unsigned int
| %llu
In file included from SimulationParameters.h:6,
from BaseCallingProfile.h:7,
from pirs_simulate.cpp:14:
InputStream.h: In constructor 'InputStream::InputStream()':
InputStream.h:50:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
50 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
InputStream.h: In constructor 'InputStream::InputStream(const char*)':
InputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
In file included from SimulationParameters.h:7:
OutputStream.h: In constructor 'OutputStream::OutputStream()':
OutputStream.h:54:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
54 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)':
OutputStream.h:58:23: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess]
58 | memset(this, 0, sizeof(*this));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/build/reproducible-path/pirs-2.0.2+dfsg/src/pirs'
make[4]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
make[4]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
make[3]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
make[2]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
dh_auto_build --sourcedirectory=src/stator/gcContCvgBias -- CC='$(CXX)'
cd src/stator/gcContCvgBias && make -j11 "INSTALL=install --strip-program=true" CC=\$\(CXX\)
make[2]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src/stator/gcContCvgBias'
g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -pedantic -Wfloat-equal self_util.cpp self_util.h
g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -pedantic -Wfloat-equal main.cpp
g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -pedantic -Wfloat-equal stat_soap_coverage.h stat_soap_coverage.cpp
self_util.cpp: In function 'char toUpper(const char&)':
self_util.cpp:182:1: warning: control reaches end of non-void function [-Wreturn-type]
182 | }
| ^
self_util.cpp: In function 'char toLower(const char&)':
self_util.cpp:190:1: warning: control reaches end of non-void function [-Wreturn-type]
190 | }
| ^
In file included from /usr/include/boost/config/header_deprecated.hpp:18,
from /usr/include/boost/progress.hpp:26,
from stat_soap_coverage.cpp:8:
/usr/include/boost/progress.hpp:27:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
27 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/timer.hpp:25:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
25 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -o gc_coverage_bias -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_TIMER_ENABLE_DEPRECATED -pedantic -Wfloat-equal self_util.o main.o stat_soap_coverage.o -Wl,-z,relro -Wl,-z,now -lgzstream -lz
make[2]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src/stator/gcContCvgBias'
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_auto_test -O--sourcedirectory=src
cd src && make -j11 check "TESTSUITEFLAGS=-j11 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
Making check in pirs
make[2]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src/pirs'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src/pirs'
make[2]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
make[2]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg/src'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedirectory=src
dh_prep -O--sourcedirectory=src
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_auto_install --sourcedirectory=src/stator/gcContCvgBias
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/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
# Fix perl interpreter path
for pl in `grep -Rl '#![/usr]*/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#![/usr]*/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg'
debian/rules override_dh_installdocs-arch
make[1]: Entering directory '/build/reproducible-path/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 '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_installdocs -O--sourcedirectory=src -Npirs
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_installchangelogs NEWS
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_installsystemduser -O--sourcedirectory=src
dh_perl -O--sourcedirectory=src
debian/rules override_dh_link-arch
make[1]: Entering directory '/build/reproducible-path/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 '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_link -O--sourcedirectory=src -Npirs
dh_strip_nondeterminism -O--sourcedirectory=src
dh_compress -O--sourcedirectory=src
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_fixperms
find debian/*/usr/lib -name "*.pl" -exec chmod +x \{\} \;
make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg'
dh_missing -O--sourcedirectory=src
dh_dwz -a -O--sourcedirectory=src
dwz: debian/pirs/usr/bin/gc_coverage_bias: .debug_info section not present
dwz: Too few files for multifile optimization
dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it.
dh_dwz: warning: Common issues include no debug information at all (missing -g) and
dh_dwz: warning: compressed debug information (#931891).
dh_strip -a -O--sourcedirectory=src
dh_makeshlibs -a -O--sourcedirectory=src
dh_shlibdeps -a -O--sourcedirectory=src
dh_installdeb -O--sourcedirectory=src
dh_gencontrol -O--sourcedirectory=src
dpkg-gencontrol: warning: package pirs: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package pirs: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -O--sourcedirectory=src
dh_builddeb -O--sourcedirectory=src
dpkg-deb: building package 'pirs' in '../pirs_2.0.2+dfsg-12_i386.deb'.
dpkg-deb: building package 'pirs-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-12_i386.deb'.
dpkg-deb: building package 'pirs-profiles' in '../pirs-profiles_2.0.2+dfsg-12_all.deb'.
dpkg-deb: building package 'pirs-examples' in '../pirs-examples_2.0.2+dfsg-12_all.deb'.
dpkg-genbuildinfo --build=binary -O../pirs_2.0.2+dfsg-12_i386.buildinfo
dpkg-genchanges --build=binary -O../pirs_2.0.2+dfsg-12_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/56832 and its subdirectories
I: Current time: Sun Feb 23 11:27:15 -12 2025
I: pbuilder-time-stamp: 1740353235
Sun Feb 23 23:27:17 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net.
Sun Feb 23 23:27:17 UTC 2025 I: Preparing to do remote build '2' on ionos6-i386.debian.net.
Sun Feb 23 23:28:12 UTC 2025 I: Deleting $TMPDIR on ionos6-i386.debian.net.
Sun Feb 23 23:28:13 UTC 2025 I: pirs_2.0.2+dfsg-12_i386.changes:
Format: 1.8
Date: Mon, 18 Dec 2023 14:39:21 +0100
Source: pirs
Binary: pirs pirs-dbgsym pirs-examples pirs-profiles
Architecture: i386 all
Version: 2.0.2+dfsg-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.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)
Closes: 1048393 1056023
Changes:
pirs (2.0.2+dfsg-12) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* Forward patch
* Fix clean target
Closes: #1048393
.
[ Étienne Mollier ]
* d/rules: define BOOST_TIMER_ENABLE_DEPRECATED.
This flag is passed to C preprocessor options to fix failure to build
from source with boost 1.83. (Closes: #1056023)
* d/control: gnuplot-qt as default gnuplot dependency.
* d/control: declare compliance to standars version 4.6.2.
* typos.patch: new: fix typos caught by lintian.
Checksums-Sha1:
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3f476b95688c5e773d07047113ffe2cc425b75c6 2565916 pirs-profiles_2.0.2+dfsg-12_all.deb
352f11e4d9f89d8370638ba69e295b5699268d0a 5600 pirs_2.0.2+dfsg-12_i386.buildinfo
537afb7f4915d1351b18b9f7565aa48ff92ced36 127716 pirs_2.0.2+dfsg-12_i386.deb
Checksums-Sha256:
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5e84c98824ccb8d9c7ecc8805158da1d04d5b2b36e68f9322d931c19e2d4a502 1948568 pirs-examples_2.0.2+dfsg-12_all.deb
3150cb2690810ac3a0a03d55dddb4e279ac09ea4b9607039d787c02facdf3a68 2565916 pirs-profiles_2.0.2+dfsg-12_all.deb
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Files:
8c66370f3933a6344a8a3a856fa91ad9 304568 debug optional pirs-dbgsym_2.0.2+dfsg-12_i386.deb
ffbb81c62973411c5b86bdab5623349b 1948568 science optional pirs-examples_2.0.2+dfsg-12_all.deb
1d9df7294df92c9c17b2c525b4e359a0 2565916 science optional pirs-profiles_2.0.2+dfsg-12_all.deb
f07ea2046b7e54575517576bbd72192d 5600 science optional pirs_2.0.2+dfsg-12_i386.buildinfo
3e14c2b0ad5e9a0b21dc18878d8ba05b 127716 science optional pirs_2.0.2+dfsg-12_i386.deb
Sun Feb 23 23:28:14 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_1-57631.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.7kzKPa5G/pirs_2.0.2+dfsg-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.7kzKPa5G/pirs_2.0.2+dfsg-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.7kzKPa5G/pirs_2.0.2+dfsg-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.7kzKPa5G/b1/pirs_2.0.2+dfsg-12_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.7kzKPa5G/b2/pirs_2.0.2+dfsg-12_i386.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 222ms
CPU time consumed: 223ms
Sun Feb 23 23:28:14 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sun Feb 23 23:28:14 UTC 2025 I: pirs from trixie built successfully and reproducibly on i386.
Sun Feb 23 23:28:16 UTC 2025 I: Submitting .buildinfo files to external archives:
Sun Feb 23 23:28:16 UTC 2025 I: Submitting 8.0K b1/pirs_2.0.2+dfsg-12_i386.buildinfo.asc
Sun Feb 23 23:28:16 UTC 2025 I: Submitting 8.0K b2/pirs_2.0.2+dfsg-12_i386.buildinfo.asc
Sun Feb 23 23:28:17 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Feb 23 23:28:17 UTC 2025 I: Done submitting .buildinfo files.
Sun Feb 23 23:28:17 UTC 2025 I: Removing signed pirs_2.0.2+dfsg-12_i386.buildinfo.asc files:
removed './b1/pirs_2.0.2+dfsg-12_i386.buildinfo.asc'
removed './b2/pirs_2.0.2+dfsg-12_i386.buildinfo.asc'