I: pbuilder: network access will be disabled during build I: Current time: Fri May 24 14:51:03 +14 2024 I: pbuilder-time-stamp: 1716511863 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [smalt_0.7.6-12.dsc] I: copying [./smalt_0.7.6.orig.tar.gz] I: copying [./smalt_0.7.6-12.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 17 04:51:58 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./smalt_0.7.6-12.dsc: no acceptable signature found dpkg-source: info: extracting smalt in smalt-0.7.6 dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz dpkg-source: info: unpacking smalt_0.7.6-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3.patch dpkg-source: info: applying add-runstatedir.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/58141/tmp/hooks/D01_modify_environment starting debug: Running on ionos16-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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 24 14:51 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/58141/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/58141/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(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 parallel=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=b0682a4ff5c74cb3b13465e7f6724132 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=58141 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.mIoM6x4B/pbuilderrc_pjAt --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mIoM6x4B/b2 --logfile b2/build.log --extrapackages usrmerge smalt_0.7.6-12.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 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Feb 13 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 2023 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 2023 more -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 May 24 14:51 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 2023 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/58141/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), zlib1g-dev, python3, samtools, libbambamc-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 ... 19604 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on libbambamc-dev; however: Package libbambamc-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} libbambamc-dev{a} libbambamc0{a} libbrotli1{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{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 publicsuffix wget 0 packages upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 28.6 MB of archives. After unpacking 104 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libbambamc0 i386 0.0.50-6+b1 [44.4 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 libbambamc-dev i386 0.0.50-6+b1 [58.2 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-8 [412 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-2 [111 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 samtools i386 1.16.1-1 [637 kB] Fetched 28.6 MB in 0s (89.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19604 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 19920 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20354 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... 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Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:i386 (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libbambamc-dev:i386 (0.0.50-6+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libcurl3-gnutls:i386 (7.88.1-8) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:i386 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up samtools (1.16.1-1) ... Processing triggers for libc-bin (2.36-9) ... 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... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/58141/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/58141/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/smalt-0.7.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../smalt_0.7.6-12_source.changes dpkg-buildpackage: info: source package smalt dpkg-buildpackage: info: source version 0.7.6-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/smalt-0.7.6' dh_auto_clean rm -rf test/*.pyc misc/*.pyc test/tmp make[1]: Leaving directory '/build/smalt-0.7.6' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/smalt-0.7.6' echo "Do nothing - fails because auf broken upstream autoconf stuff" Do nothing - fails because auf broken upstream autoconf stuff make[1]: Leaving directory '/build/smalt-0.7.6' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/smalt-0.7.6' dh_auto_configure -- CONFIG_SHELL=/bin/bash ./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 CONFIG_SHELL=/bin/bash checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for icc... no checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for ranlib... ranlib checking for a Python interpreter with version >= 2.6... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.1 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.1/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.1/site-packages checking for samtools... yes checking for sam_open in -lbam... no checking for BAMBAMC... yes checking for gzread in -lz... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking semaphore.h usability... yes checking semaphore.h presence... yes checking for semaphore.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking emmintrin.h usability... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating test/data/Makefile config.status: creating misc/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/smalt-0.7.6' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/smalt-0.7.6' dh_auto_build -a make -j15 make[2]: Entering directory '/build/smalt-0.7.6' make all-recursive make[3]: Entering directory '/build/smalt-0.7.6' Making all in src make[4]: Entering directory '/build/smalt-0.7.6/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c elib.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c filio.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c hashidx.c: In function 'countPerfectKey': hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter] 191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ hashidx.c: In function 'countCollisionKey': hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter] 206 | static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ diffstr.c: In function 'diffStrGetDiffStats': diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress] 978 | if (diffstrp+1 != NULL) { | ^~ hashidx.c: In function 'collectWords': hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter] 223 | static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ hashidx.c: In function 'countWords': hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter] 265 | static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ sequence.c: In function 'seqFastqGetConstSequence': sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2079 | if (length) | ^~ sequence.c:2081:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2081 | return NULL; | ^~~~~~ sequence.c: In function 'seqFastqGetSequence': sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2094 | if (length) | ^~ sequence.c:2096:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2096 | return NULL; | ^~~~~~ hashidx.c: At top level: hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function] 446 | static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp) | ^~~~~~~~~~~~ hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=] 63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file"; | ^~~~~~~~~~~~~~~~~~~~~ sequence.c: In function 'seqIOopen': sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=] 489 | strcpy(p->fmode, "r"); | ^~~~~~~~~~~~~~~~~~~~~ sequence.c:491:3: note: here 491 | case SEQIO_WRITE_GZIP_FASTA: | ^~~~ segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function] 1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs) | ^~~~~~~~~~~~~~~~~~~~~~ segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function] 1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=] 49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */ | ^~~~~~ smalt.c: In function 'cleanupSmaltOutput': smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) | ^~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c rm -f libseq.a ar cru libseq.a elib.o filio.o sequence.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseq.a rm -f libsgm.a ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-swsimd.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libsgm.a gcc -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz make[4]: Leaving directory '/build/smalt-0.7.6/src' Making all in test make[4]: Entering directory '/build/smalt-0.7.6/test' make[5]: Entering directory '/build/smalt-0.7.6/test' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/smalt-0.7.6/test' make[4]: Leaving directory '/build/smalt-0.7.6/test' Making all in misc make[4]: Entering directory '/build/smalt-0.7.6/misc' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c simread.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c rsample.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c fetchseq.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c splitreads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c mixreads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c splitmates.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c readstats.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c trunkreads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c basqcol.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c basqual.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c simqual.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c ../src/diffstr.c: In function 'diffStrGetDiffStats': ../src/diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress] 978 | if (diffstrp+1 != NULL) { | ^~ gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz gcc -I../src/ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz make[4]: Leaving directory '/build/smalt-0.7.6/misc' make[4]: Entering directory '/build/smalt-0.7.6' make[4]: Leaving directory '/build/smalt-0.7.6' make[3]: Leaving directory '/build/smalt-0.7.6' make[2]: Leaving directory '/build/smalt-0.7.6' make -C test sequenceReverseComplement_test make[2]: Entering directory '/build/smalt-0.7.6/test' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c sequenceReverseComplement_test.c gcc -I../src/ -I../test -Wall -Wextra -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz make[2]: Leaving directory '/build/smalt-0.7.6/test' make[1]: Leaving directory '/build/smalt-0.7.6' dh_auto_build -Nsmalt make -j15 make[1]: Entering directory '/build/smalt-0.7.6' make all-recursive make[2]: Entering directory '/build/smalt-0.7.6' Making all in src make[3]: Entering directory '/build/smalt-0.7.6/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/smalt-0.7.6/src' Making all in test make[3]: Entering directory '/build/smalt-0.7.6/test' make[4]: Entering directory '/build/smalt-0.7.6/test' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/smalt-0.7.6/test' make[3]: Leaving directory '/build/smalt-0.7.6/test' Making all in misc make[3]: Entering directory '/build/smalt-0.7.6/misc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/smalt-0.7.6/misc' make[3]: Entering directory '/build/smalt-0.7.6' make[3]: Leaving directory '/build/smalt-0.7.6' make[2]: Leaving directory '/build/smalt-0.7.6' make[1]: Leaving directory '/build/smalt-0.7.6' dh_auto_test make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/smalt-0.7.6' Making check in src make[2]: Entering directory '/build/smalt-0.7.6/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/smalt-0.7.6/src' Making check in test make[2]: Entering directory '/build/smalt-0.7.6/test' make[3]: Entering directory '/build/smalt-0.7.6/test' make sequenceReverseComplement_test smalt_Xali_test make[4]: Entering directory '/build/smalt-0.7.6/test' make[4]: 'sequenceReverseComplement_test' is up to date. gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-smalt.o `test -f '../src/smalt.c' || echo './'`../src/smalt.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c ../src/smalt.c: In function 'cleanupSmaltOutput': ../src/smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ gcc -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -ffile-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt_Xali_test smalt_Xali_test-smalt.o smalt_Xali_test-menu.o smalt_Xali_test-threads.o smalt_Xali_test-infmt.o smalt_Xali_test-results.o smalt_Xali_test-resultpairs.o smalt_Xali_test-insert.o smalt_Xali_test-report.o smalt_Xali_test-rmap.o ../src/libsgm.a ../src/libseq.a -lbambamc -lz -lm -lpthread -lz make[4]: Leaving directory '/build/smalt-0.7.6/test' make check-TESTS make[4]: Entering directory '/build/smalt-0.7.6/test' PASS: splitReads_test.py PASS: results_split_test.py PASS: ouform_cigar_test.py PASS: sample_test.py PASS: cigar_test.py PASS: mthread_test.py PASS: ioform_test.py PASS: xali_test.py PASS: bam_cigar_test.py ================== All 9 tests passed ================== make[4]: Leaving directory '/build/smalt-0.7.6/test' make[3]: Leaving directory '/build/smalt-0.7.6/test' make[2]: Leaving directory '/build/smalt-0.7.6/test' Making check in misc make[2]: Entering directory '/build/smalt-0.7.6/misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/smalt-0.7.6/misc' make[2]: Entering directory '/build/smalt-0.7.6' make[2]: Leaving directory '/build/smalt-0.7.6' make[1]: Leaving directory '/build/smalt-0.7.6' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/smalt-0.7.6' # upstream install does install more files than needed make[1]: Leaving directory '/build/smalt-0.7.6' debian/rules override_dh_install-indep make[1]: Entering directory '/build/smalt-0.7.6' dh_install # fix path to smalt executable in examples for py in `ls test/*.py` ; do \ sed 's#PROGNAM = "../src/smalt"#PROGNAM = "/usr/bin/smalt"#' ${py} > debian/smalt-examples/usr/share/doc/smalt/${py} ; \ done make[1]: Leaving directory '/build/smalt-0.7.6' dh_install -Nsmalt-examples dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/smalt/usr/bin/smalt: DWARF compression not beneficial - old size 241487 new size 245166 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'smalt' in '../smalt_0.7.6-12_i386.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-12_i386.deb'. dpkg-deb: building package 'smalt-examples' in '../smalt-examples_0.7.6-12_all.deb'. dpkg-genbuildinfo --build=binary -O../smalt_0.7.6-12_i386.buildinfo dpkg-genchanges --build=binary -O../smalt_0.7.6-12_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/58141/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/58141/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/58141 and its subdirectories I: Current time: Fri May 24 14:53:57 +14 2024 I: pbuilder-time-stamp: 1716512037