Sat Aug 21 13:57:51 UTC 2021 I: starting to build smalt/bullseye/armhf on jenkins on '2021-08-21 13:57' Sat Aug 21 13:57:51 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_8/11195/console.log Sat Aug 21 13:57:51 UTC 2021 I: Downloading source for bullseye/smalt=0.7.6-9 --2021-08-21 13:57:51-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/smalt/smalt_0.7.6-9.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2064 (2.0K) Saving to: ‘smalt_0.7.6-9.dsc’ 0K .. 100% 53.7M=0s 2021-08-21 13:57:51 (53.7 MB/s) - ‘smalt_0.7.6-9.dsc’ saved [2064/2064] Sat Aug 21 13:57:52 UTC 2021 I: smalt_0.7.6-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: smalt Binary: smalt, smalt-examples Architecture: any all Version: 0.7.6-9 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://www.sanger.ac.uk/science/tools/smalt-0 Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/smalt Vcs-Git: https://salsa.debian.org/med-team/smalt.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 12), zlib1g-dev, python3, samtools, libbambamc-dev Package-List: smalt deb science optional arch=any smalt-examples deb science optional arch=all Checksums-Sha1: bfe5beaf8334b78ee7e98571c954a4b12d915895 72290533 smalt_0.7.6.orig.tar.gz 468175d34aca747ee1930d3bb0b81c43ff636767 8756 smalt_0.7.6-9.debian.tar.xz Checksums-Sha256: 89ccdfe471edba3577b43de9ebfdaedb5cd6e26b02bf4000c554253433796b31 72290533 smalt_0.7.6.orig.tar.gz c6e7a6c2864ed46919540d4ec094b169047bf0a047e0556c63174822682ffd79 8756 smalt_0.7.6-9.debian.tar.xz Files: c3215d70ba960c8fdc8e80191695c60b 72290533 smalt_0.7.6.orig.tar.gz 71b35e810b52016cbdc695ef6f82a0cc 8756 smalt_0.7.6-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl4PmOMACgkQPCZ2P2xn 5uJspA//dRztcMEp0v8iqLNi1xcR3SAKE6Og01/tv4QjFVYamzXF3t5TOD9/ccdu jjJSUrXrSFSal8PcU5uMjxjPhsqajoaFThcmLi5YhODIAIkTz58eNyO1XlLy1rSh oVORV0Xf7bCVKHGg9EemE+kdQOhK6gMShoxmZQIjngZI0bsqAsUhQ87JRMI4QPQs GJU+qAn2cMg/56DXm7XrowZjIpvWAW0TnXUzTDaf8Q6/IyMjQ2EZNV9kocfM1qcM M6t7IivANYzfw0dEodley1kmyHiY8hPrATyrzVbWOXGJvQ+hAaKz9yMt2bTruWv4 kT8BiyBioUIcFrK8iT+O6RfRReu3jSWqWyZCaSEu3KNq2zZt5eJcgeBaRKOQw1Ph 4uNSVCJM7Bu/8vxIAHfL9tOwpNpMCQfwqWS+xzFt9n9QOijeg53d6ptkX6zF/a9O m+HN8OtVtvrLHBmL5j64703/sbWnBi6G1SluB3lhYOwusazscAQ4BGkOjyj7VTmM 4sRjK3p/S6qZZZFRKpbOtDvJVBCT1S0E8KHaXftTKoL8JgcoEPLYKl/CimPaXEkI ZBzfWH3n8GQnoSZmPKSi9UIIlCV1j4f0P0+UL28ZZkJqhwBOY+FgLlHZfN41C7nP WJ//B11mgmQm3OlnoI5ydaLCe5HM0Fe0fcEXlsZDSLh+QnyacUI= =HQ1s -----END PGP SIGNATURE----- Sat Aug 21 13:57:52 UTC 2021 I: Checking whether the package is not for us Sat Aug 21 13:57:52 UTC 2021 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Sat Aug 21 13:57:52 UTC 2021 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Sat Aug 21 14:19:11 UTC 2021 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 21 01:58:08 -12 2021 I: pbuilder-time-stamp: 1629554288 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [smalt_0.7.6-9.dsc] I: copying [./smalt_0.7.6.orig.tar.gz] I: copying [./smalt_0.7.6-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.xuEx6pUV/trustedkeys.kbx': General error gpgv: Signature made Fri Jan 3 07:41:23 2020 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./smalt_0.7.6-9.dsc 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_0.7.6-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/22966/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='30fd96de4fcc415d985399354bb2baf7' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='22966' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.LBlVTGRJBw/pbuilderrc_92Th --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.LBlVTGRJBw/b1 --logfile b1/build.log smalt_0.7.6-9.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux virt64a 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 20 21:25 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/22966/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 (= 12), 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 ... 19398 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 (= 12); 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} libglib2.0-0{a} libhts3{a} libicu67{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{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} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-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 libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 26.4 MB of archives. After unpacking 89.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf libpython3.9-minimal armhf 3.9.2-1 [790 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf python3.9-minimal armhf 3.9.2-1 [1630 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libmpdec3 armhf 2.5.1-1 [74.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf libpython3.9-stdlib armhf 3.9.2-1 [1608 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf python3.9 armhf 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf python3 armhf 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libbambamc0 armhf 0.0.50-4 [30.7 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf libbambamc-dev armhf 0.0.50-4 [43.2 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+b1 [306 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf samtools armhf 1.11-1 [519 kB] Fetched 26.4 MB in 4s (7366 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../3-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:armhf. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_armhf.deb ... Unpacking libpython3.9-minimal:armhf (3.9.2-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../6-libexpat1_2.2.10-2_armhf.deb ... Unpacking libexpat1:armhf (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_armhf.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:armhf (3.9.2-1) ... Setting up libexpat1:armhf (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20265 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:armhf. 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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 ... 20686 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_armhf.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. 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Selecting previously unselected package libicu67:armhf. Preparing to unpack .../21-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../22-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../23-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../24-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../25-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../26-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libbambamc0. Preparing to unpack .../27-libbambamc0_0.0.50-4_armhf.deb ... Unpacking libbambamc0 (0.0.50-4) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../28-libglib2.0-0_2.66.8-1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.66.8-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../29-pkg-config_0.29.2-1_armhf.deb ... Unpacking pkg-config (0.29.2-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../30-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Selecting previously unselected package libbambamc-dev. Preparing to unpack .../31-libbambamc-dev_0.0.50-4_armhf.deb ... Unpacking libbambamc-dev (0.0.50-4) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../32-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../33-libsasl2-modules-db_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../34-libsasl2-2_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../35-libldap-2.4-2_2.4.57+dfsg-3_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../36-libnghttp2-14_1.43.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.43.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../37-libpsl5_0.21.0-1.2_armhf.deb ... Unpacking libpsl5:armhf (0.21.0-1.2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../38-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../39-libssh2-1_1.9.0-2_armhf.deb ... Unpacking libssh2-1:armhf (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../40-libcurl3-gnutls_7.74.0-1.3+b1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../41-libdeflate0_1.7-1_armhf.deb ... Unpacking libdeflate0:armhf (1.7-1) ... Selecting previously unselected package libhts3:armhf. Preparing to unpack .../42-libhts3_1.11-4_armhf.deb ... Unpacking libhts3:armhf (1.11-4) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../43-libncurses6_6.2+20201114-2_armhf.deb ... Unpacking libncurses6:armhf (6.2+20201114-2) ... Selecting previously unselected package samtools. Preparing to unpack .../44-samtools_1.11-1_armhf.deb ... Unpacking samtools (1.11-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up libpsl5:armhf (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:armhf (1.0.9-2+b2) ... Setting up libnghttp2-14:armhf (1.43.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up libdeflate0:armhf (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:armhf (6.2+20201114-2) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up libbambamc0 (0.0.50-4) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libmpdec3:armhf (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:armhf (1.9.0-2) ... Setting up libelf1:armhf (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libbambamc-dev (0.0.50-4) ... Setting up libreadline8:armhf (8.1-1) ... Setting up libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:armhf (3.9.2-1) ... Setting up libpython3-stdlib:armhf (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:armhf (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Processing triggers for libc-bin (2.31-13) ... 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... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/smalt-0.7.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../smalt_0.7.6-9_source.changes dpkg-buildpackage: info: source package smalt dpkg-buildpackage: info: source version 0.7.6-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot 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 build dh build 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' # see upstream INSTALL file CONFIG_SHELL=/bin/bash /bin/bash ./configure 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... /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... gcc3 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... 3.9 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.9/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.9/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... /bin/grep checking for egrep... /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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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' dh_auto_build make -j3 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' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT elib.o -MD -MP -MF .deps/elib.Tpo -c -o elib.o elib.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT filio.o -MD -MP -MF .deps/filio.Tpo -c -o filio.o filio.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT sequence.o -MD -MP -MF .deps/sequence.Tpo -c -o sequence.o sequence.c sequence.c: In function 'seqFastqGetConstSequence': sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2079 | if (length) | ^~ sequence.c:2081:2: 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:2096:2: 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: | ^~~~ mv -f .deps/filio.Tpo .deps/filio.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-score.o -MD -MP -MF .deps/libsgm_a-score.Tpo -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c 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 */ | ^~~~~~ mv -f .deps/elib.Tpo .deps/elib.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-diffstr.o -MD -MP -MF .deps/libsgm_a-diffstr.Tpo -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c mv -f .deps/libsgm_a-score.Tpo .deps/libsgm_a-score.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-alibuffer.o -MD -MP -MF .deps/libsgm_a-alibuffer.Tpo -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c mv -f .deps/libsgm_a-alibuffer.Tpo .deps/libsgm_a-alibuffer.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-alignment.o -MD -MP -MF .deps/libsgm_a-alignment.Tpo -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) | ^~~~~~~~~~~~~ mv -f .deps/libsgm_a-alignment.Tpo .deps/libsgm_a-alignment.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-sort.o -MD -MP -MF .deps/libsgm_a-sort.Tpo -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c mv -f .deps/libsgm_a-diffstr.Tpo .deps/libsgm_a-diffstr.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-array.o -MD -MP -MF .deps/libsgm_a-array.Tpo -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c mv -f .deps/libsgm_a-array.Tpo .deps/libsgm_a-array.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-interval.o -MD -MP -MF .deps/libsgm_a-interval.Tpo -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/libsgm_a-interval.Tpo .deps/libsgm_a-interval.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashidx.o -MD -MP -MF .deps/libsgm_a-hashidx.Tpo -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) | ~~~~~~~~~~^~~~~~~~ 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"; | ^~~~~~~~~~~~~~~~~~~~~ mv -f .deps/libsgm_a-sort.Tpo .deps/libsgm_a-sort.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashhit.o -MD -MP -MF .deps/libsgm_a-hashhit.Tpo -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c mv -f .deps/sequence.Tpo .deps/sequence.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-segment.o -MD -MP -MF .deps/libsgm_a-segment.Tpo -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c 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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/libsgm_a-hashidx.Tpo .deps/libsgm_a-hashidx.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-smalt.o -MD -MP -MF .deps/smalt-smalt.Tpo -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) | ~~~~~~~~^~~~~~~ mv -f .deps/libsgm_a-hashhit.Tpo .deps/libsgm_a-hashhit.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-menu.o -MD -MP -MF .deps/smalt-menu.Tpo -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c mv -f .deps/libsgm_a-segment.Tpo .deps/libsgm_a-segment.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-threads.o -MD -MP -MF .deps/smalt-threads.Tpo -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c mv -f .deps/smalt-smalt.Tpo .deps/smalt-smalt.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-infmt.o -MD -MP -MF .deps/smalt-infmt.Tpo -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c mv -f .deps/smalt-infmt.Tpo .deps/smalt-infmt.Po mv -f .deps/smalt-threads.Tpo .deps/smalt-threads.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-results.o -MD -MP -MF .deps/smalt-results.Tpo -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 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-resultpairs.o -MD -MP -MF .deps/smalt-resultpairs.Tpo -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c mv -f .deps/smalt-menu.Tpo .deps/smalt-menu.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-report.o -MD -MP -MF .deps/smalt-report.Tpo -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c results.c: In function 'resultSetInferInsertSize': results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare] 2470 | rp->sidx == rp->sidx) { | ^~ mv -f .deps/smalt-resultpairs.Tpo .deps/smalt-resultpairs.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-rmap.o -MD -MP -MF .deps/smalt-rmap.Tpo -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c mv -f .deps/smalt-report.Tpo .deps/smalt-report.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-insert.o -MD -MP -MF .deps/smalt-insert.Tpo -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c mv -f .deps/smalt-rmap.Tpo .deps/smalt-rmap.Po 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') mv -f .deps/smalt-results.Tpo .deps/smalt-results.Po ranlib libsgm.a mv -f .deps/smalt-insert.Tpo .deps/smalt-insert.Po gcc -Wall -Wextra -g -O2 -fdebug-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[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' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT simread.o -MD -MP -MF .deps/simread.Tpo -c -o simread.o simread.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT rsample.o -MD -MP -MF .deps/rsample.Tpo -c -o rsample.o rsample.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT fetchseq.o -MD -MP -MF .deps/fetchseq.Tpo -c -o fetchseq.o fetchseq.c mv -f .deps/rsample.Tpo .deps/rsample.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT splitreads.o -MD -MP -MF .deps/splitreads.Tpo -c -o splitreads.o splitreads.c mv -f .deps/fetchseq.Tpo .deps/fetchseq.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT mixreads.o -MD -MP -MF .deps/mixreads.Tpo -c -o mixreads.o mixreads.c mv -f .deps/splitreads.Tpo .deps/splitreads.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT splitmates.o -MD -MP -MF .deps/splitmates.Tpo -c -o splitmates.o splitmates.c mv -f .deps/splitmates.Tpo .deps/splitmates.Po mv -f .deps/mixreads.Tpo .deps/mixreads.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT readstats.o -MD -MP -MF .deps/readstats.Tpo -c -o readstats.o readstats.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT trunkreads.o -MD -MP -MF .deps/trunkreads.Tpo -c -o trunkreads.o trunkreads.c mv -f .deps/readstats.Tpo .deps/readstats.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqcol.o -MD -MP -MF .deps/basqcol.Tpo -c -o basqcol.o basqcol.c mv -f .deps/trunkreads.Tpo .deps/trunkreads.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqual.o -MD -MP -MF .deps/basqual.Tpo -c -o basqual.o basqual.c mv -f .deps/basqcol.Tpo .deps/basqcol.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT simqual.o -MD -MP -MF .deps/simqual.Tpo -c -o simqual.o simqual.c mv -f .deps/simread.Tpo .deps/simread.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT diffstr.o -MD -MP -MF .deps/diffstr.Tpo -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c mv -f .deps/basqual.Tpo .deps/basqual.Po gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 mv -f .deps/simqual.Tpo .deps/simqual.Po gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 mv -f .deps/diffstr.Tpo .deps/diffstr.Po gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-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[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 -j3 check 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' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT sequenceReverseComplement_test.o -MD -MP -MF .deps/sequenceReverseComplement_test.Tpo -c -o sequenceReverseComplement_test.o sequenceReverseComplement_test.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-smalt.o -MD -MP -MF .deps/smalt_Xali_test-smalt.Tpo -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 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-menu.o -MD -MP -MF .deps/smalt_Xali_test-menu.Tpo -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.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) | ~~~~~~~~^~~~~~~ mv -f .deps/sequenceReverseComplement_test.Tpo .deps/sequenceReverseComplement_test.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-threads.o -MD -MP -MF .deps/smalt_Xali_test-threads.Tpo -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c mv -f .deps/smalt_Xali_test-threads.Tpo .deps/smalt_Xali_test-threads.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-infmt.o -MD -MP -MF .deps/smalt_Xali_test-infmt.Tpo -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c mv -f .deps/smalt_Xali_test-infmt.Tpo .deps/smalt_Xali_test-infmt.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-results.o -MD -MP -MF .deps/smalt_Xali_test-results.Tpo -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c mv -f .deps/smalt_Xali_test-smalt.Tpo .deps/smalt_Xali_test-smalt.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-resultpairs.o -MD -MP -MF .deps/smalt_Xali_test-resultpairs.Tpo -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c ../src/results.c: In function 'resultSetInferInsertSize': ../src/results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare] 2470 | rp->sidx == rp->sidx) { | ^~ mv -f .deps/smalt_Xali_test-menu.Tpo .deps/smalt_Xali_test-menu.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-insert.o -MD -MP -MF .deps/smalt_Xali_test-insert.Tpo -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c mv -f .deps/smalt_Xali_test-resultpairs.Tpo .deps/smalt_Xali_test-resultpairs.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-report.o -MD -MP -MF .deps/smalt_Xali_test-report.Tpo -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c mv -f .deps/smalt_Xali_test-insert.Tpo .deps/smalt_Xali_test-insert.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-rmap.o -MD -MP -MF .deps/smalt_Xali_test-rmap.Tpo -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c mv -f .deps/smalt_Xali_test-results.Tpo .deps/smalt_Xali_test-results.Po gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-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 mv -f .deps/smalt_Xali_test-report.Tpo .deps/smalt_Xali_test-report.Po mv -f .deps/smalt_Xali_test-rmap.Tpo .deps/smalt_Xali_test-rmap.Po gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-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 fakeroot debian/rules binary dh binary dh_testroot 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 dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'smalt' in '../smalt_0.7.6-9_armhf.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-9_armhf.deb'. dpkg-deb: building package 'smalt-examples' in '../smalt-examples_0.7.6-9_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../smalt_0.7.6-9_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: 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/22966 and its subdirectories I: Current time: Sat Aug 21 02:16:12 -12 2021 I: pbuilder-time-stamp: 1629555372 Sat Aug 21 14:19:13 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ff4a-armhf-rb.debian.net. Sat Aug 21 14:19:13 UTC 2021 I: Preparing to do remote build '2' on ff4a-armhf-rb.debian.net. Sat Aug 21 15:06:22 UTC 2021 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. Sat Aug 21 15:06:25 UTC 2021 I: smalt_0.7.6-9_armhf.changes: Format: 1.8 Date: Fri, 03 Jan 2020 11:44:39 +0100 Source: smalt Binary: smalt smalt-dbgsym smalt-examples Architecture: armhf all Version: 0.7.6-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: smalt - Sequence Mapping and Alignment Tool smalt-examples - Sequence Mapping and Alignment Tool (examples) Closes: 938501 Changes: smalt (0.7.6-9) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * Use 2to3 to port to Python3 Closes: #938501 * debhelper-compat 12 * Standards-Version: 4.4.1 * Remove trailing whitespace in debian/changelog * Use secure URI in debian/watch. * Use secure URI in Homepage field. * Set upstream metadata fields: Archive, Bug-Submit. * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g . [ Michael R. Crusoe ] * Fixed the remaining Python3 issues in test scripts Checksums-Sha1: 5847fe05066058a2483bb0cbc1a806d072bb7edf 372844 smalt-dbgsym_0.7.6-9_armhf.deb 675bff33b31fbae6858413b7d86bdc694fdeba29 71870924 smalt-examples_0.7.6-9_all.deb c23ffe774fe548308d1dfb10fa92f78b397bc390 6135 smalt_0.7.6-9_armhf.buildinfo ac819d1a853a9f7bf71e442a4bb8a397973d56ca 97596 smalt_0.7.6-9_armhf.deb Checksums-Sha256: 5890fe2040daaaadc53e32c755912c1230707300ae9528ac49a5e4c714d70206 372844 smalt-dbgsym_0.7.6-9_armhf.deb 7994a25339f0990ad4941c9f880a0cb3ad21ec9af602211fb02c8d84c8a561fb 71870924 smalt-examples_0.7.6-9_all.deb 54df0f2f6a20db46a3ba40fe9d76153fe7143db1a7cc86124451d74838615480 6135 smalt_0.7.6-9_armhf.buildinfo 59a7bb30181448bfa7b59d3060ddd8fb86aca56d534e05d4ff60b9014c3f59ad 97596 smalt_0.7.6-9_armhf.deb Files: dc028600b32af700d93b610d0e635120 372844 debug optional smalt-dbgsym_0.7.6-9_armhf.deb 545dd5558d7479db8b5e69e2e00f9118 71870924 science optional smalt-examples_0.7.6-9_all.deb 76280b2bbb4bedc78e30a6b4f69cb5ce 6135 science optional smalt_0.7.6-9_armhf.buildinfo 5f4b2367010431bcf5e031cbf237d7c3 97596 science optional smalt_0.7.6-9_armhf.deb Sat Aug 21 15:06:27 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.LBlVTGRJBw/smalt_0.7.6-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.LBlVTGRJBw/smalt_0.7.6-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.LBlVTGRJBw/smalt_0.7.6-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.LBlVTGRJBw/b1/smalt_0.7.6-9_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.LBlVTGRJBw/b2/smalt_0.7.6-9_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.394s) 1.394s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.926s) 0.926s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sat Aug 21 15:06:29 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sat Aug 21 15:06:29 UTC 2021 I: smalt from bullseye built successfully and reproducibly on armhf. Sat Aug 21 15:06:32 UTC 2021 I: Submitting .buildinfo files to external archives: Sat Aug 21 15:06:32 UTC 2021 I: Submitting 8.0K b1/smalt_0.7.6-9_armhf.buildinfo.asc Sat Aug 21 15:06:33 UTC 2021 I: Submitting 8.0K b2/smalt_0.7.6-9_armhf.buildinfo.asc Sat Aug 21 15:06:33 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Aug 21 15:06:33 UTC 2021 I: Done submitting .buildinfo files. Sat Aug 21 15:06:33 UTC 2021 I: Removing signed smalt_0.7.6-9_armhf.buildinfo.asc files: removed './b1/smalt_0.7.6-9_armhf.buildinfo.asc' removed './b2/smalt_0.7.6-9_armhf.buildinfo.asc'