I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 15 17:23:26 +14 2025 I: pbuilder-time-stamp: 1749957806 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 gpgv: Signature made Tue Dec 19 08:43:26 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pirs_2.0.2+dfsg-12.dsc: no acceptable signature found 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/2115699/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 15 03:23 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2115699/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2115699/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=0975788f65864aa696c5026226351689 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2115699 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.FoMZtiW1/pbuilderrc_zpDY --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FoMZtiW1/b2 --logfile b2/build.log pirs_2.0.2+dfsg-12.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 12 17:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2115699/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: arm64 Maintainer: Debian Pbuilder Team 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 ... 19745 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} libsub-override-perl{a} libtool{a} libuchardet0{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 30.2 MB of archives. After unpacking 238 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-2.1+b1 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 33 http://deb.debian.org/debian trixie/main arm64 libgzstream0 arm64 1.5+git20171107.9a20658-2 [7288 B] Get: 34 http://deb.debian.org/debian trixie/main arm64 libgzstream-dev arm64 1.5+git20171107.9a20658-2 [7488 B] Get: 35 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Fetched 30.2 MB in 0s (176 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19745 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../30-libboost1.83-dev_1.83.0-2.1+b1_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-2.1+b1) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../31-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libgzstream0:arm64. Preparing to unpack .../32-libgzstream0_1.5+git20171107.9a20658-2_arm64.deb ... Unpacking libgzstream0:arm64 (1.5+git20171107.9a20658-2) ... Selecting previously unselected package libgzstream-dev:arm64. Preparing to unpack .../33-libgzstream-dev_1.5+git20171107.9a20658-2_arm64.deb ... Unpacking libgzstream-dev:arm64 (1.5+git20171107.9a20658-2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../34-zlib1g-dev_1%3a1.3.dfsg-3.1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libboost1.83-dev:arm64 (1.83.0-2.1+b1) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up libgzstream0:arm64 (1.5+git20171107.9a20658-2) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libgzstream-dev:arm64 (1.5+git20171107.9a20658-2) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-10) ... 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: user script /srv/workspace/pbuilder/2115699/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2115699/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/pirs-2.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 incompatibilities. 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=aarch64-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/aarch64-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 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 $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for gzopen in -lz... yes checking Whether to include support for 'pirs diploid' command... yes checking Whether to include support for 'pirs simulate' command... yes checking Whether to include support for multiple threads... yes checking for g++ option to support OpenMP... -fopenmp checking Whether to include support for SSE2 instructions... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating pirs/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/pirs-2.0.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg' dh_auto_build cd src && make -j12 make[2]: Entering directory '/build/reproducible-path/pirs-2.0.2+dfsg/src' (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh '/build/reproducible-path/pirs-2.0.2+dfsg/src/missing' autoheader) rm -f stamp-h1 touch config.h.in cd . && /bin/sh ./config.status config.h config.status: creating config.h config.status: config.h is unchanged 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -c -o GCBiasProfile.o GCBiasProfile.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" | ^~~~~~~~ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -c -o pirs_simulate.o pirs_simulate.cpp 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 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 { | ^~~~~~~~~~~ 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 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 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 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 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 { | ^~~~~~~~~~~~ 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 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 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 { | ^~~~~~~~~~~~ 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 -mbranch-protection=standard -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 -j12 "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 or instead.' 27 | BOOST_HEADER_DEPRECATED( "the facilities in or " ) | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/timer.hpp:25:1: note: '#pragma message: This header is deprecated. Use the facilities in instead.' 25 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ 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 -j12 check "TESTSUITEFLAGS=-j12 --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_arm64.deb'. dpkg-deb: building package 'pirs-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-12_arm64.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_arm64.buildinfo dpkg-genchanges --build=binary -O../pirs_2.0.2+dfsg-12_arm64.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: user script /srv/workspace/pbuilder/2115699/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2115699/tmp/hooks/B01_cleanup finished 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/2115699 and its subdirectories I: Current time: Sun Jun 15 17:24:29 +14 2025 I: pbuilder-time-stamp: 1749957869