I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 22 01:58:00 +14 2024 I: pbuilder-time-stamp: 1713700680 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [smalt_0.7.6-13.dsc] I: copying [./smalt_0.7.6.orig.tar.gz] I: copying [./smalt_0.7.6-13.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jan 12 06:08:11 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./smalt_0.7.6-13.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_0.7.6-13.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/25728/tmp/hooks/D01_modify_environment starting debug: Running on virt32b. 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 Apr 21 11:59 /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/25728/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/25728/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=de6ecde857564ffb856c444b76dd3beb LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=25728 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.0Hmw7CN3/pbuilderrc_Hvkk --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0Hmw7CN3/b2 --logfile b2/build.log smalt_0.7.6-13.dsc' SUDO_GID=112 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:14 /bin -> usr/bin I: user script /srv/workspace/pbuilder/25728/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: armhf 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 ... 19635 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} netbase{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} tzdata{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, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 27.3 MB of archives. After unpacking 96.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.8-1 [802 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.8-1 [1707 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-3 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.8-1 [1709 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libbambamc0 armhf 0.0.50-6+b1 [32.7 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-1+b2 [31.9 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf pkg-config armhf 1.8.1-1+b2 [14.0 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libbambamc-dev armhf 0.0.50-6+b1 [45.1 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libcurl3-gnutls armhf 8.5.0-2 [378 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libhts3 armhf 1.19+ds-1 [394 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.4+20240113-1 [81.8 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf samtools armhf 1.19.2-1 [614 kB] Fetched 27.3 MB in 1s (36.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19635 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.8-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_armhf.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:armhf (3.11.8-1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... 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 ... 19951 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_armhf.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../5-libreadline8_8.2-3+b1_armhf.deb ... Unpacking libreadline8:armhf (8.2-3+b1) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_armhf.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... 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 ... 20939 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.6-1_armhf.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../03-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.190-1+b1_armhf.deb ... Unpacking libelf1:armhf (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../25-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... 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Selecting previously unselected package samtools. Preparing to unpack .../51-samtools_1.19.2-1_armhf.deb ... Unpacking samtools (1.19.2-1) ... Setting up libhtscodecs2:armhf (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libpsl5:armhf (0.21.2-1+b1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libnghttp2-14:armhf (1.59.0-1) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 21 12:02:22 UTC 2024. Universal Time is now: Sun Apr 21 12:02:22 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-1+b2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:armhf (6.4+20240113-1) ... Setting up libbambamc0:armhf (0.0.50-6+b1) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1:armhf (1.11.0-4) ... Setting up netbase (6.4) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libreadline8:armhf (8.2-3+b1) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Setting up pkgconf:armhf (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (1.8.1-1+b2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libbambamc-dev:armhf (0.0.50-6+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.8-1) ... Setting up libcurl3-gnutls:armhf (8.5.0-2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libhts3:armhf (1.19+ds-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up samtools (1.19.2-1) ... Processing triggers for libc-bin (2.37-15) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/25728/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/25728/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/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_0.7.6-13_source.changes dpkg-buildpackage: info: source package smalt dpkg-buildpackage: info: source version 0.7.6-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' dh_auto_clean rm -rf test/*.pyc misc/*.pyc test/tmp find . -type d -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_clean debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/smalt-0.7.6' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' dh_auto_configure -- CONFIG_SHELL=/bin/bash ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... no checking emmintrin.h presence... no checking for emmintrin.h... no checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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/reproducible-path/smalt-0.7.6' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' dh_auto_build -a make -j4 make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6' make all-recursive make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6' Making all in src make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sequence.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c sequence.c: In function 'make3BitMangledCodec': sequence.c:298:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare] 298 | for (i=1; iOUTBUFSIZE) linewidth = OUTBUFSIZE; | ^ 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; | ^~~~~~ 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: | ^~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c 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) { | ^~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c 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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.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) | ~~~~~~~~~~^~~~~~~~ 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) | ~~~~~~~~~~^~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c 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"; | ^~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c hashhit.c: In function 'hashCreateHitList': hashhit.c:1559:18: warning: comparison of integer expressions of different signedness: 'int' and 'enum ' [-Wsign-compare] 1559 | if (maxnhits < HITLST_MINSIZ) maxnhits = HITLST_MINSIZ; | ^ 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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c smalt.c: In function 'cleanupSmaltOutput': smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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-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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6/src' Making all in test make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[5]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' Making all in misc make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6/misc' make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6' make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make -C test sequenceReverseComplement_test make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sequenceReverseComplement_test.c gcc -I../src/ -I../test -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6/test' make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_auto_build -Nsmalt make -j4 make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' make all-recursive make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6' Making all in src make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src' Making all in test make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' Making all in misc make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc' make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6' make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_auto_test make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' Making check in src make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src' Making check in test make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make sequenceReverseComplement_test smalt_Xali_test make[4]: Entering directory '/build/reproducible-path/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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.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 -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c gcc -I../src/ -I../test -Wall -Wextra -g -O2 -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/smalt-0.7.6/test' make check-TESTS make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/smalt-0.7.6/test' make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' Making check in misc make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc' make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6' make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' # upstream install does install more files than needed make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'smalt' in '../smalt_0.7.6-13_armhf.deb'. dpkg-deb: building package 'smalt-examples' in '../smalt-examples_0.7.6-13_all.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_armhf.deb'. dpkg-genbuildinfo --build=binary -O../smalt_0.7.6-13_armhf.buildinfo dpkg-genchanges --build=binary -O../smalt_0.7.6-13_armhf.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/25728/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/25728/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/25728 and its subdirectories I: Current time: Mon Apr 22 02:17:35 +14 2024 I: pbuilder-time-stamp: 1713701855