unshare: unshare failed: Cannot allocate memory W: pbuilder: unshare CLONE_NEWNET not available I: pbuilder: network access is available during build! I: Current time: Fri Jun 25 02:07:33 -12 2021 I: pbuilder-time-stamp: 1624630053 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [pirs_2.0.2+dfsg-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.ySBr4Bdt/trustedkeys.kbx': General error gpgv: Signature made Fri Dec 4 23:14:30 2020 -12 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/4762/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='ae717e34051d434ca132a6a37e3c8312' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4762' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.RCDTyXttLg/pbuilderrc_NfbR --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RCDTyXttLg/b1 --logfile b1/build.log pirs_2.0.2+dfsg-9.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos12-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-1 (2021-06-10) i686 GNU/Linux I: ls -l /bin total 5784 -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jun 23 21:28 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/4762/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team 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 ... 19675 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 28.3 MB of archives. After unpacking 210 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 34 http://deb.debian.org/debian bullseye/main i386 libgzstream0 i386 1.5+dfsg-5 [6896 B] Get: 35 http://deb.debian.org/debian bullseye/main i386 libgzstream-dev i386 1.5+dfsg-5 [7188 B] Get: 36 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Fetched 28.3 MB in 15s (1842 kB/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 ... 19675 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.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_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../07-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../10-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_i386.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_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../23-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../25-libicu67_67.1-6_i386.deb ... Unpacking libicu67:i386 (67.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_i386.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:i386. Preparing to unpack .../31-libboost1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-dev:i386. Preparing to unpack .../32-libboost-dev_1.74.0.3_i386.deb ... Unpacking libboost-dev:i386 (1.74.0.3) ... Selecting previously unselected package libgzstream0. Preparing to unpack .../33-libgzstream0_1.5+dfsg-5_i386.deb ... Unpacking libgzstream0 (1.5+dfsg-5) ... Selecting previously unselected package libgzstream-dev. Preparing to unpack .../34-libgzstream-dev_1.5+dfsg-5_i386.deb ... Unpacking libgzstream-dev (1.5+dfsg-5) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../35-zlib1g-dev_1%3a1.2.11.dfsg-2_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libboost1.74-dev:i386 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:i386 (67.1-6) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libgzstream0 (1.5+dfsg-5) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libelf1:i386 (0.183-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgzstream-dev (1.5+dfsg-5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/pirs-2.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b 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 i386 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=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-pirs-diploid --disable-sse2 checking for a BSD-compatible install... /usr/bin/install -c checking whether 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 $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for gzopen in -lz... yes checking Whether to include support for 'pirs diploid' command... yes checking Whether to include support for 'pirs simulate' command... yes checking Whether to include support for multiple threads... yes checking for g++ option to support OpenMP... -fopenmp checking Whether to include support for SSE2 instructions... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating pirs/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/pirs-2.0.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/pirs-2.0.2+dfsg' dh_auto_build cd src && make -j10 make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src' (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash '/build/pirs-2.0.2+dfsg/src/missing' autoheader) rm -f stamp-h1 touch config.h.in cd . && /bin/bash ./config.status config.h config.status: creating config.h config.status: config.h is unchanged make all-recursive make[3]: Entering directory '/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 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]); | ^ 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 { | ^~~~~~~~~~~~ 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 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 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 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 { | ^~~~~~~~~~~ IndelProfile.cpp: In function 'void load_indel_info_line(char*, Profile&)': IndelProfile.cpp:117:44: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] 117 | } else if (sscanf(line, "Read_1_Count = %lu", &n) == 1) | ~~^ ~~ | | | | | uint64_t* {aka long long unsigned int*} | long unsigned int* | %llu IndelProfile.cpp:119:42: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] 119 | else if (sscanf(line, "Read_2_Count = %lu", &n) == 1) | ~~^ ~~ | | | | | uint64_t* {aka long long unsigned int*} | long unsigned int* | %llu IndelProfile.cpp: In constructor 'IndelProfile::IndelProfile(const SimulationParameters&)': IndelProfile.cpp:165:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 165 | info(" read_1_count = %lu\n", read_1_count); | ~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long long unsigned int} | long unsigned int | %llu IndelProfile.cpp:166:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 166 | info(" read_2_count = %lu\n", read_2_count); | ~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long long unsigned int} | long unsigned int | %llu In file included from 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 { | ^~~~~~~~~~~ util.cpp: In function 'void* xmalloc(size_t)': util.cpp:192:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 192 | fatal_error("Out of memory: tried to allocate %lu bytes", size); | ~~^ ~~~~ | | | | | size_t {aka unsigned int} | long unsigned int | %u util.cpp: In function 'void* xrealloc(void*, size_t)': util.cpp:200:53: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 200 | fatal_error("Out of memory: tried to reallocate %lu bytes", size); | ~~^ ~~~~ | | | | | size_t {aka unsigned int} | long unsigned int | %u 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 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 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 { | ^~~~~~~~~~~~ pirs_diploid.cpp: In function 'bool try_indel(const double*, const size_t*, const std::vector&, size_t&, std::vector&, bool, const char*, Counter&)': pirs_diploid.cpp:435:32: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 435 | indel_log_file.printf("%s\t%zu\t%zu\t%c\t%zu\t", | ~~^ | | | unsigned int | %llu 436 | id, log_ref_seq_idx, log_diploid_seq_idx, | ~~~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} pirs_diploid.cpp:435:37: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 435 | indel_log_file.printf("%s\t%zu\t%zu\t%c\t%zu\t", | ~~^ | | | unsigned int | %llu 436 | id, log_ref_seq_idx, log_diploid_seq_idx, | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} 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 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 -j10 "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 -j10 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_i386.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_i386.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_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/4762 and its subdirectories I: Current time: Fri Jun 25 02:14:47 -12 2021 I: pbuilder-time-stamp: 1624630487