I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 28 08:19:37 +14 2023 I: pbuilder-time-stamp: 1690481977 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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-9.dsc] I: copying [./pirs_2.0.2+dfsg.orig.tar.xz] I: copying [./pirs_2.0.2+dfsg-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.s8r7B9t8/trustedkeys.kbx': General error gpgv: Signature made Sun Dec 6 01:14:30 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pirs_2.0.2+dfsg-9.dsc 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-9.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1206865/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. 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 Jul 28 08:19 /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/1206865/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1206865/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6620fefbaebc48cbbe9331ae5f5c1e45 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=1206865 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.JkgEboqo/pbuilderrc_LJkN --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JkgEboqo/b2 --logfile b2/build.log pirs_2.0.2+dfsg-9.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-1 (2023-07-14) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 21 2022 more -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 9 Jul 28 08:19 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 21 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/1206865/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 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 ... 19707 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} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgzstream-dev{a} libgzstream0{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{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, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 28.1 MB of archives. After unpacking 210 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libgzstream0 amd64 1.5+dfsg-5 [6712 B] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libgzstream-dev amd64 1.5+dfsg-5 [6876 B] Get: 36 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Fetched 28.1 MB in 2s (12.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../10-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../23-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../25-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../31-libboost1.74-dev_1.74.0-9_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0-9) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../32-libboost-dev_1.74.0.3_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libgzstream0. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1206865/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/1206865/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/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-9_source.changes dpkg-buildpackage: info: source package pirs dpkg-buildpackage: info: source version 2.0.2+dfsg-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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/pirs-2.0.2+dfsg' dh_auto_clean cd src && ./srclean.sh >/dev/null 2>/dev/null || true make[1]: Leaving directory '/build/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/pirs-2.0.2+dfsg' cd src && \ mv INSTALL INSTALL.save && \ autoreconf --install && \ mv INSTALL.save INSTALL && \ cd /build/pirs-2.0.2+dfsg configure.ac:9: installing './compile' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' Makefile.am: installing './INSTALL' pirs/Makefile.am:28: warning: source file 'SFMT-src-1.4/SFMT.c' is in a subdirectory, pirs/Makefile.am:28: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. pirs/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/pirs-2.0.2+dfsg' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/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 build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for gzopen in -lz... yes checking Whether to include support for 'pirs diploid' command... yes checking Whether to include support for 'pirs simulate' command... yes checking Whether to include support for multiple threads... yes checking for g++ option to support OpenMP... -fopenmp checking Whether to include support for SSE2 instructions... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating pirs/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/pirs-2.0.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/pirs-2.0.2+dfsg' dh_auto_build cd src && make -j15 make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src' (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh '/build/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/pirs-2.0.2+dfsg/src' Making all in pirs make[4]: Entering directory '/build/pirs-2.0.2+dfsg/src/pirs' g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InputStream.o InputStream.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputStream.o OutputStream.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.o util.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mt19937-64.o mt19937-64.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_diploid.o pirs_diploid.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o BaseCallingProfile.o BaseCallingProfile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskQvalsByEamss.o MaskQvalsByEamss.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Profile.o Profile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp main.cpp:18:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" | ^~~~~~~~ main.cpp:18:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" | ^~~~~~~~ pirs_diploid.cpp:639:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 639 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ pirs_diploid.cpp:639:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 639 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ pirs_diploid.cpp:639:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 639 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ pirs_diploid.cpp:641:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 641 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ pirs_diploid.cpp:641:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 641 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ pirs_diploid.cpp:641:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 641 | info(" %#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ pirs_diploid.cpp:643:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 643 | 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:672:18: 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:700:23: 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:1235:10: 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:1235:29: 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:1540:21: 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:1557:2: 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:1574:20: 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:1579:19: 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:1685:26: 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:1713:7: 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:1714:7: 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:1715:7: 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:1716:7: 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:1717:7: 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:1717:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); | ^~~~~~~~ pirs_simulate.cpp:1717:44: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); | ^~~~~~~~ pirs_simulate.cpp:1764:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 1764 | info("Bases in reference sequences: %"PRIu64"\n", | ^ pirs_simulate.cpp:1766:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 1766 | info("Read pairs simulated: %"PRIu64"\n", | ^ pirs_simulate.cpp:1768:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 1768 | info("Bases in reads: %"PRIu64"\n", | ^ pirs_simulate.cpp:1773:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 1773 | info("Substitution error count: %"PRIu64"\n", | ^ pirs_simulate.cpp:1777:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 1777 | info("Insertion count: %"PRIu64"\n", | ^ pirs_simulate.cpp:1779:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 1779 | info("Deletion count: %"PRIu64"\n", | ^ pirs_simulate.cpp:1795:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 1795 | info("Bases masked by EAMSS algorithm: %"PRIu64"\n", counters.masked_bases); | ^ pirs_simulate.cpp:1856:8: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 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:50:32: 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:54:32: 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 OutputStream.cpp:1: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:32: 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:58:32: 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:11: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: 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:54:32: 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:12: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:32: 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:58:32: 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 InputStream.cpp:1: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: 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:54:32: 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:50:32: 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:54:32: 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:50:32: 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:54:32: 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, from BaseCallingProfile.h:7, from BaseCallingProfile.cpp:5: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:32: 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:58:32: 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:50:32: 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:54:32: 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, from GCBiasProfile.h:5, from GCBiasProfile.cpp:5: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:32: 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:58:32: 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:50:32: 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:54:32: 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, from IndelProfile.cpp:2: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:32: 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:58:32: 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:50:32: 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:54:32: 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, from BaseCallingProfile.h:7, from pirs_simulate.cpp:14: OutputStream.h: In constructor 'OutputStream::OutputStream()': OutputStream.h:54:32: 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:58:32: 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 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o pirs InputStream.o OutputStream.o main.o util.o mt19937-64.o pirs_diploid.o BaseCallingProfile.o GCBiasProfile.o IndelProfile.o MaskQvalsByEamss.o Profile.o pirs_simulate.o -lz -lz make[4]: Leaving directory '/build/pirs-2.0.2+dfsg/src/pirs' make[4]: Entering directory '/build/pirs-2.0.2+dfsg/src' make[4]: Leaving directory '/build/pirs-2.0.2+dfsg/src' make[3]: Leaving directory '/build/pirs-2.0.2+dfsg/src' make[2]: Leaving directory '/build/pirs-2.0.2+dfsg/src' dh_auto_build --sourcedirectory=src/stator/gcContCvgBias -- CC='$(CXX)' cd src/stator/gcContCvgBias && make -j15 "INSTALL=install --strip-program=true" CC=\$\(CXX\) make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src/stator/gcContCvgBias' g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal self_util.cpp self_util.h g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal main.cpp g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal stat_soap_coverage.h stat_soap_coverage.cpp 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:22, from stat_soap_coverage.cpp:8: /usr/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in or instead.' 23 | BOOST_HEADER_DEPRECATED( "the facilities in or " ) | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in instead.' 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o gc_coverage_bias -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal self_util.o main.o stat_soap_coverage.o -Wl,-z,relro -Wl,-z,now -lgzstream -lz make[2]: Leaving directory '/build/pirs-2.0.2+dfsg/src/stator/gcContCvgBias' make[1]: Leaving directory '/build/pirs-2.0.2+dfsg' dh_auto_test -O--sourcedirectory=src cd src && make -j15 check VERBOSE=1 make[1]: Entering directory '/build/pirs-2.0.2+dfsg/src' Making check in pirs make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src/pirs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/pirs-2.0.2+dfsg/src/pirs' make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src' make[2]: Leaving directory '/build/pirs-2.0.2+dfsg/src' make[1]: Leaving directory '/build/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/pirs-2.0.2+dfsg' dh_auto_install --sourcedirectory=src/stator/gcContCvgBias make[1]: Leaving directory '/build/pirs-2.0.2+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/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/pirs-2.0.2+dfsg' debian/rules override_dh_installdocs-arch make[1]: Entering directory '/build/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/pirs-2.0.2+dfsg' dh_installdocs -O--sourcedirectory=src -Npirs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pirs-2.0.2+dfsg' dh_installchangelogs NEWS make[1]: Leaving directory '/build/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/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/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/pirs-2.0.2+dfsg' dh_fixperms find debian/*/usr/lib -name "*.pl" -exec chmod +x \{\} \; make[1]: Leaving directory '/build/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-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-9_amd64.deb'. dpkg-deb: building package 'pirs-examples' in '../pirs-examples_2.0.2+dfsg-9_all.deb'. dpkg-deb: building package 'pirs' in '../pirs_2.0.2+dfsg-9_amd64.deb'. dpkg-deb: building package 'pirs-profiles' in '../pirs-profiles_2.0.2+dfsg-9_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pirs_2.0.2+dfsg-9_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: user script /srv/workspace/pbuilder/1206865/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1206865/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/1206865 and its subdirectories I: Current time: Fri Jul 28 08:24:41 +14 2023 I: pbuilder-time-stamp: 1690482281