I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 21 19:31:02 +14 2022 I: pbuilder-time-stamp: 1655789462 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 [discosnp_4.4.4-1.dsc] I: copying [./discosnp_4.4.4.orig.tar.gz] I: copying [./discosnp_4.4.4-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.i8OKCjEd/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 2 02:57:13 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 ./discosnp_4.4.4-1.dsc dpkg-source: info: extracting discosnp in discosnp-4.4.4 dpkg-source: info: unpacking discosnp_4.4.4.orig.tar.gz dpkg-source: info: unpacking discosnp_4.4.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_gatb-core.patch dpkg-source: info: applying no_install_to_wrong_dir.patch dpkg-source: info: applying path_to_readme_file_names.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying adapt_test_scripts.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying shell_syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24244/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. 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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/24244/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/24244/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]="i686-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=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=894eb88dbe7e4354938ddfe379f85326 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=24244 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/tmp.MqjotJPQ7W/pbuilderrc_fN0l --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.MqjotJPQ7W/b2 --logfile b2/build.log --extrapackages usrmerge discosnp_4.4.4-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Feb 25 2021 bash -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash -rwxr-xr-x 1 root root 124904 Sep 23 2020 date -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd -rwxr-xr-x 1 root root 100752 Sep 23 2020 df -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir -rwxr-xr-x 1 root root 83644 Feb 8 2021 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 34664 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln -rwxr-xr-x 1 root root 55572 Feb 8 2020 login -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 8 2021 more -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Feb 25 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jun 21 19:31 sh -> bash lrwxrwxrwx 1 root root 4 Jun 20 05:47 sh.distrib -> dash -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty -rwsr-xr-x 1 root root 79396 Feb 8 2021 su -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch -rwxr-xr-x 1 root root 34664 Sep 23 2020 true -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/24244/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), dh-python, python3, cmake, libgatbcore-dev, libboost-dev, libhdf5-dev, zlib1g-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 ... 19674 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 dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libgatbcore-dev; however: Package libgatbcore-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgatbcore-dev{a} libgatbcore3{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp24{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} procps{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 57.1 MB of archives. After unpacking 370 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 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libprocps8 i386 2:3.3.17-5 [64.2 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 procps i386 2:3.3.17-5 [501 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 cmake-data all 3.18.4-2 [1725 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.6 [727 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libarchive13 i386 3.4.3-2+b1 [384 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-2 [244 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libcurl4 i386 7.74.0-1.2 [372 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libjsoncpp24 i386 1.9.4-4 [86.1 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 librhash0 i386 1.4.1-2 [144 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libuv1 i386 1.40.0-1 [139 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 cmake i386 3.18.4-2 [7029 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 hdf5-helpers i386 1.10.6+repack-2 [40.0 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libaec0 i386 1.0.4-1 [22.6 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libsz2 i386 1.0.4-1 [6820 B] Get: 68 http://deb.debian.org/debian bullseye/main i386 libaec-dev i386 1.0.4-1 [21.5 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 71 http://deb.debian.org/debian bullseye/main i386 libgatbcore3 i386 1.4.2+dfsg-6 [1871 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libgatbcore-dev i386 1.4.2+dfsg-6 [4027 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libhdf5-103-1 i386 1.10.6+repack-2 [1153 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libhdf5-cpp-103-1 i386 1.10.6+repack-2 [152 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libhdf5-fortran-102 i386 1.10.6+repack-2 [112 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-100 i386 1.10.6+repack-2 [93.2 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-fortran-100 i386 1.10.6+repack-2 [57.0 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-cpp-100 i386 1.10.6+repack-2 [37.7 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo-dev i386 1:2.0.6-4 [299 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libjpeg-dev i386 1:2.0.6-4 [67.8 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libhdf5-dev i386 1.10.6+repack-2 [2594 kB] Fetched 57.1 MB in 1s (92.5 MB/s) debconf: delaying package configuration, since apt-utils is not 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Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libpsl5:i386 (0.21.0-1.2) ... 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 hdf5-helpers (1.10.6+repack-2) ... 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 libbrotli1:i386 (1.0.9-2+b2) ... Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libaec0:i386 (1.0.4-1) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:i386 (1.40.0-1) ... Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libjpeg62-turbo-dev:i386 (1:2.0.6-4) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:i386 (6.2+20201114-2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libgatbcore3:i386 (1.4.2+dfsg-6) ... Setting up libjsoncpp24:i386 (1.9.4-4) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up librhash0:i386 (1.4.1-2) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up cmake-data (3.18.4-2) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.6) ... Setting up libprocps8:i386 (2:3.3.17-5) ... Setting up libsz2:i386 (1.0.4-1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:i386 (3.4.3-2+b1) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libaec-dev:i386 (1.0.4-1) ... Setting up libjpeg-dev:i386 (1:2.0.6-4) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-2) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgatbcore-dev:i386 (1.4.2+dfsg-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up libhdf5-103-1:i386 (1.10.6+repack-2) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libhdf5-cpp-103-1:i386 (1.10.6+repack-2) ... Setting up libcurl4:i386 (7.74.0-1.2) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up libhdf5-hl-100:i386 (1.10.6+repack-2) ... 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 libhdf5-hl-cpp-100:i386 (1.10.6+repack-2) ... Setting up libhdf5-fortran-102:i386 (1.10.6+repack-2) ... Setting up cmake (3.18.4-2) ... Setting up libhdf5-hl-fortran-100:i386 (1.10.6+repack-2) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libhdf5-dev (1.10.6+repack-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/i386-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Processing triggers for libc-bin (2.31-11) ... 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 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.4 kB of archives. After this operation, 156 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 24 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.4 kB in 0s (4029 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 41735 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_24_all.deb ... Unpacking usrmerge (24) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (24) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package I: Running cd /build/discosnp-4.4.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package discosnp dpkg-buildpackage: info: source version 4.4.4-1 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 --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- gatb-core is here '/build/discosnp-4.4.4/thirdparty/gatb-core' CMake Warning (dev) at /usr/lib/i386-linux-gnu/cmake/GatbCore.cmake:39 (add_subdirectory): The source directory /build/discosnp-4.4.4/thirdparty/gatb-core does not contain a CMakeLists.txt file. CMake does not support this case but it used to work accidentally and is being allowed for compatibility. Policy CMP0014 is not set: Input directories must have CMakeLists.txt. Run "cmake --help-policy CMP0014" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:47 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/discosnp-4.4.4/obj-i686-linux-gnu dh_auto_build cd obj-i686-linux-gnu && make -j18 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' /usr/bin/cmake -S/build/discosnp-4.4.4 -B/build/discosnp-4.4.4/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/discosnp-4.4.4/obj-i686-linux-gnu/CMakeFiles /build/discosnp-4.4.4/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/depend make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/depend make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/kissnp2 /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake --color= make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/kissreads2 /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/QHC /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/read_file_names /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/create_coverage_h5_file /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake --color= Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend.internal". Scanning dependencies of target quick_hierarchical_clustering Scanning dependencies of target read_file_names Scanning dependencies of target create_coverage_h5_file Scanning dependencies of target kissnp2 make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/build make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/build make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build Scanning dependencies of target kissreads2 make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' [ 4%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o [ 8%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/read_file_names/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /build/discosnp-4.4.4/tools/read_file_names/src/get_read_file_names.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Filter.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Filter.cpp [ 13%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o [ 17%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o [ 21%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/commons.cpp [ 26%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Bubble.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/create_coverage_h5_file/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -c /build/discosnp-4.4.4/tools/create_coverage_h5_file/src/create_coverage_h5_file.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/QHC/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -c /build/discosnp-4.4.4/tools/QHC/src/quick_hierarchical_clustering.cpp [ 30%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o [ 34%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o [ 39%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/couple.cpp.o [ 43%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Kissnp2.cpp [ 52%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o [ 52%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/main.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/main.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/Kissreads2.cpp [ 56%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/couple.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/couple.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/extension_algorithm.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/fragment_index.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/fragment_info.cpp [ 60%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o [ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/libchash.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/interface_libchash.cpp [ 69%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/list.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/libchash.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp [ 73%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/list.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/list.cpp [ 78%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/main.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/main.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/outputs.cpp /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro 'READ_UL' 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1216:4: note: in expansion of macro 'LOAD_AND_RETURN' 1216 | LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); | ^~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro 'READ_UL' 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1221:4: note: in expansion of macro 'LOAD_AND_RETURN' 1221 | LOAD_AND_RETURN(ht, ht->posLastFind); | ^~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro 'READ_UL' 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1285:7: note: in expansion of macro 'LOAD_AND_RETURN' 1285 | { LOAD_AND_RETURN(ht, retval);} | ^~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro 'READ_UL' 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1295:8: note: in expansion of macro 'LOAD_AND_RETURN' 1295 | {LOAD_AND_RETURN(ht, retval);} | ^~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1402:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | fread(szMagicKey, 1, 4, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1411:4: note: in expansion of macro 'READ_UL' 1411 | READ_UL(fp, ht->cchKey); | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1412:4: note: in expansion of macro 'READ_UL' 1412 | READ_UL(fp, ht->cItems); | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1413:4: note: in expansion of macro 'READ_UL' 1413 | READ_UL(fp, ht->cDeletedItems); | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1416:4: note: in expansion of macro 'READ_UL' 1416 | READ_UL(fp, cchKey); | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1418:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1418 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1423:7: note: in expansion of macro 'READ_UL' 1423 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:617:4: note: in expansion of macro 'READ_UL' 617 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:622:3: note: in expansion of macro 'READ_UL' 622 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ [ 82%] Linking CXX executable ../../bin/quick_hierarchical_clustering cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC && /usr/bin/cmake -E cmake_link_script CMakeFiles/quick_hierarchical_clustering.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -o ../../bin/quick_hierarchical_clustering -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' [ 82%] Built target quick_hierarchical_clustering [ 86%] Linking CXX executable ../../bin/read_file_names cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names && /usr/bin/cmake -E cmake_link_script CMakeFiles/read_file_names.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -o ../../bin/read_file_names -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' [ 86%] Built target read_file_names [ 91%] Linking CXX executable ../../bin/create_coverage_h5_file cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file && /usr/bin/cmake -E cmake_link_script CMakeFiles/create_coverage_h5_file.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -o ../../bin/create_coverage_h5_file -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' [ 91%] Built target create_coverage_h5_file [ 95%] Linking CXX executable ../../bin/kissreads2 cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissreads2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o CMakeFiles/kissreads2.dir/src/commons.cpp.o CMakeFiles/kissreads2.dir/src/couple.cpp.o CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o CMakeFiles/kissreads2.dir/src/libchash.cpp.o CMakeFiles/kissreads2.dir/src/list.cpp.o CMakeFiles/kissreads2.dir/src/main.cpp.o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -o ../../bin/kissreads2 -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz [100%] Linking CXX executable ../../bin/kissnp2 cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' [100%] Built target kissreads2 make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' [100%] Built target kissnp2 make[2]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/discosnp-4.4.4/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-i686-linux-gnu && make -j18 install DESTDIR=/build/discosnp-4.4.4/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' /usr/bin/cmake -S/build/discosnp-4.4.4 -B/build/discosnp-4.4.4/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/kissnp2 -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/kissnp2" to "" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/kissreads2 -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/kissreads2" to "" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/quick_hierarchical_clustering -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/quick_hierarchical_clustering" to "" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/read_file_names -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/read_file_names" to "" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/create_coverage_h5_file -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/create_coverage_h5_file" to "" make[1]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/discosnp-4.4.4' dh_install mkdir -p debian/discosnp/usr/lib/discosnp/bin mv debian/discosnp/usr/bin/read_file_names debian/discosnp/usr/lib/discosnp/bin mv debian/discosnp/usr/bin/quick_hierarchical_clustering debian/discosnp/usr/lib/discosnp/bin rm -rf debian/discosnp/usr/share/discosnp/scripts/jenkins make[1]: Leaving directory '/build/discosnp-4.4.4' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/discosnp-4.4.4' dh_installman # dh_installman interprets .sh as language - just copy manpages manually cp -a debian/mans/*.sh.1 debian/discosnp/usr/share/man/man1 make[1]: Leaving directory '/build/discosnp-4.4.4' dh_python3 I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/create_filtered_vcf.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/vcf_formatting_functions.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_common.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_compacted_int_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_compacted_paths_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_msr_to_gfa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_node_ids_to_node_sequences.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'discosnp' in '../discosnp_4.4.4-1_i386.deb'. dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_4.4.4-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../discosnp_4.4.4-1_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: copying local configuration I: user script /srv/workspace/pbuilder/24244/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/24244/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/24244 and its subdirectories I: Current time: Tue Jun 21 19:31:46 +14 2022 I: pbuilder-time-stamp: 1655789506