Fri Feb 28 18:23:16 UTC 2025 I: starting to build pirs/trixie/amd64 on jenkins on '2025-02-28 18:23'
Fri Feb 28 18:23:16 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_24/49869/console.log
Fri Feb 28 18:23:16 UTC 2025 I: Downloading source for trixie/pirs=2.0.2+dfsg-12
--2025-02-28 18:23:16-- 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% 370M=0s
2025-02-28 18:23:16 (370 MB/s) - ‘pirs_2.0.2+dfsg-12.dsc’ saved [2123/2123]
Fri Feb 28 18:23:16 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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Fri Feb 28 18:23:16 UTC 2025 I: Checking whether the package is not for us
Fri Feb 28 18:23:16 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Fri Feb 28 18:23:16 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Fri Feb 28 18:24:13 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu Apr 2 12:46:18 -12 2026
I: pbuilder-time-stamp: 1775177178
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: 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/19777/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='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='15663bb5afed4adf86bc2c92c9a9dfb7'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
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='19777'
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.r2sW82rG/pbuilderrc_OEAg --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.r2sW82rG/b1 --logfile b1/build.log pirs_2.0.2+dfsg-12.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/19777/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: amd64
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 ... 19802 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 32.1 MB of archives. After unpacking 240 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libgzstream0 amd64 1.5+git20171107.9a20658-3 [7032 B]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libgzstream-dev amd64 1.5+git20171107.9a20658-3 [7332 B]
Get: 35 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Fetched 32.1 MB in 3s (11.8 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
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(Reading database ... 19802 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
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Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
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Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
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Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ...
Unpacking file (1:5.45-3+b1) ...
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Unpacking gettext-base (0.23.1-1) ...
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Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.8-1+b2) ...
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Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libpipeline1:amd64 (1.5.8-1) ...
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Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
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:amd64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up libgzstream0:amd64 (1.5+git20171107.9a20658-3) ...
Setting up zlib1g-dev:amd64 (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:amd64 (0.0.8-1+b2) ...
Setting up libboost-dev:amd64 (1.83.0.2+b2) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
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:amd64 (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 amd64
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=x86_64-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/x86_64-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 -j42
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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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",
| ^
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 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 {
| ^~~~~~~~~~~
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 {
| ^~~~~~~~~~~
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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
OutputStream.h:33:7: note: 'class OutputStream' declared here
33 | class OutputStream {
| ^~~~~~~~~~~~
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 {
| ^~~~~~~~~~~
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 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 {
| ^~~~~~~~~~~
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: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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
InputStream.h:25:7: note: 'class InputStream' declared here
25 | class InputStream {
| ^~~~~~~~~~~
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: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 {
| ^~~~~~~~~~~~
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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -j42 "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 -j42 check "TESTSUITEFLAGS=-j42 --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_amd64.deb'.
dpkg-deb: building package 'pirs-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-12_amd64.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_amd64.buildinfo
dpkg-genchanges --build=binary -O../pirs_2.0.2+dfsg-12_amd64.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/19777 and its subdirectories
I: Current time: Thu Apr 2 12:47:12 -12 2026
I: pbuilder-time-stamp: 1775177232
Fri Feb 28 18:24:13 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Fri Feb 28 18:24:13 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Fri Feb 28 18:26:56 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Fri Feb 28 18:26:56 UTC 2025 I: pirs_2.0.2+dfsg-12_amd64.changes:
Format: 1.8
Date: Mon, 18 Dec 2023 14:39:21 +0100
Source: pirs
Binary: pirs pirs-dbgsym pirs-examples pirs-profiles
Architecture: amd64 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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659e354fdc81bb5ec4bf20a619571edc2c374c29 1948568 pirs-examples_2.0.2+dfsg-12_all.deb
3f476b95688c5e773d07047113ffe2cc425b75c6 2565916 pirs-profiles_2.0.2+dfsg-12_all.deb
8e11df30e2288ebd415b9957a73891fd4e61fa47 5676 pirs_2.0.2+dfsg-12_amd64.buildinfo
47f1ff2a38e7068cae28c40f358561de5e034663 121456 pirs_2.0.2+dfsg-12_amd64.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
c42ea1b6c4c64f71ffe85a6a1d4c8e9c0ff51b2819183a71a1c1cb658bbd78b7 5676 pirs_2.0.2+dfsg-12_amd64.buildinfo
461105f7ce2a2cbd3e3839152231389a78d42ee6fd1a855896dd4bd826afad7d 121456 pirs_2.0.2+dfsg-12_amd64.deb
Files:
e87a0b1fd0dea34771df80341f8862d3 315624 debug optional pirs-dbgsym_2.0.2+dfsg-12_amd64.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
c22483bf6924f3083c14115c12e4d47a 5676 science optional pirs_2.0.2+dfsg-12_amd64.buildinfo
0b32f933e0b55e64db7ebaa6dccaae23 121456 science optional pirs_2.0.2+dfsg-12_amd64.deb
Fri Feb 28 18:26:57 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_24-49869.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.r2sW82rG/pirs_2.0.2+dfsg-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.r2sW82rG/pirs_2.0.2+dfsg-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.r2sW82rG/pirs_2.0.2+dfsg-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.r2sW82rG/b1/pirs_2.0.2+dfsg-12_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.r2sW82rG/b2/pirs_2.0.2+dfsg-12_amd64.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: 263ms
CPU time consumed: 245ms
Fri Feb 28 18:26:58 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Fri Feb 28 18:26:58 UTC 2025 I: pirs from trixie built successfully and reproducibly on amd64.
Fri Feb 28 18:26:59 UTC 2025 I: Submitting .buildinfo files to external archives:
Fri Feb 28 18:26:59 UTC 2025 I: Submitting 8.0K b1/pirs_2.0.2+dfsg-12_amd64.buildinfo.asc
Fri Feb 28 18:27:00 UTC 2025 I: Submitting 8.0K b2/pirs_2.0.2+dfsg-12_amd64.buildinfo.asc
Fri Feb 28 18:27:02 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Fri Feb 28 18:27:02 UTC 2025 I: Done submitting .buildinfo files.
Fri Feb 28 18:27:02 UTC 2025 I: Removing signed pirs_2.0.2+dfsg-12_amd64.buildinfo.asc files:
removed './b1/pirs_2.0.2+dfsg-12_amd64.buildinfo.asc'
removed './b2/pirs_2.0.2+dfsg-12_amd64.buildinfo.asc'