Sun Aug 15 13:18:26 UTC 2021 I: starting to build smalt/bullseye/arm64 on jenkins on '2021-08-15 13:18' Sun Aug 15 13:18:26 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_24/22764/console.log Sun Aug 15 13:18:26 UTC 2021 I: Downloading source for bullseye/smalt=0.7.6-9 --2021-08-15 13:18:26-- 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% 156M=0s 2021-08-15 13:18:26 (156 MB/s) - ‘smalt_0.7.6-9.dsc’ saved [2064/2064] Sun Aug 15 13:18:26 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----- Sun Aug 15 13:18:27 UTC 2021 I: Checking whether the package is not for us Sun Aug 15 13:18:27 UTC 2021 I: Starting 1st build on remote node codethink14-arm64.debian.net. Sun Aug 15 13:18:27 UTC 2021 I: Preparing to do remote build '1' on codethink14-arm64.debian.net. Sun Aug 15 13:30:10 UTC 2021 I: Deleting $TMPDIR on codethink14-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Aug 15 01:19:04 -12 2021 I: pbuilder-time-stamp: 1629033544 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.2K0OcdX3/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/24436/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='24436' 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.rVSPVMP5a0/pbuilderrc_EmvJ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.rVSPVMP5a0/b1 --logfile b1/build.log smalt_0.7.6-9.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink14-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 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 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 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 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 134808 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 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 13 21:25 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 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/24436/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: arm64 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 ... 19646 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 27.2 MB of archives. After unpacking 98.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libbambamc0 arm64 0.0.50-4 [33.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libbambamc-dev arm64 0.0.50-4 [47.0 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Fetched 27.2 MB in 1s (18.4 MB/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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... 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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 ... 20513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.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:arm64. 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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 ... 20934 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_arm64.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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Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../39-libssh2-1_1.9.0-2_arm64.deb ... Unpacking libssh2-1:arm64 (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:arm64. Preparing to unpack .../40-libcurl3-gnutls_7.74.0-1.3+b1_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../41-libdeflate0_1.7-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.7-1) ... Selecting previously unselected package libhts3:arm64. Preparing to unpack .../42-libhts3_1.11-4_arm64.deb ... Unpacking libhts3:arm64 (1.11-4) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../43-libncurses6_6.2+20201114-2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2) ... Selecting previously unselected package samtools. Preparing to unpack .../44-samtools_1.11-1_arm64.deb ... Unpacking samtools (1.11-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up libpsl5:arm64 (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:arm64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libsigsegv2:arm64 (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:arm64 (2.1.27+dfsg-2.1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:arm64 (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:arm64 (8.1-1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:arm64 (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:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (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:arm64 (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 arm64 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 -j8 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 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 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 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 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 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 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; | ^~~~~~ mv -f .deps/libsgm_a-alibuffer.Tpo .deps/libsgm_a-alibuffer.Po 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 -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 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 */ | ^~~~~~ 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-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-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-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-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-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/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-segment.o -MD -MP -MF .deps/libsgm_a-segment.Tpo -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.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 smalt-smalt.o -MD -MP -MF .deps/smalt-smalt.Tpo -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.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-sort.Tpo .deps/libsgm_a-sort.Po 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 smalt-menu.o -MD -MP -MF .deps/smalt-menu.Tpo -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 -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 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-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 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/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-results.o -MD -MP -MF .deps/smalt-results.Tpo -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c mv -f .deps/smalt-infmt.Tpo .deps/smalt-infmt.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-resultpairs.o -MD -MP -MF .deps/smalt-resultpairs.Tpo -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.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-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-report.o -MD -MP -MF .deps/smalt-report.Tpo -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c 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-rmap.o -MD -MP -MF .deps/smalt-rmap.Tpo -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.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-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-smalt.Tpo .deps/smalt-smalt.Po mv -f .deps/smalt-resultpairs.Tpo .deps/smalt-resultpairs.Po mv -f .deps/smalt-menu.Tpo .deps/smalt-menu.Po mv -f .deps/sequence.Tpo .deps/sequence.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') ranlib libsgm.a mv -f .deps/smalt-insert.Tpo .deps/smalt-insert.Po mv -f .deps/smalt-rmap.Tpo .deps/smalt-rmap.Po mv -f .deps/smalt-report.Tpo .deps/smalt-report.Po mv -f .deps/smalt-results.Tpo .deps/smalt-results.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 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 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 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 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/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 basqual.o -MD -MP -MF .deps/basqual.Tpo -c -o basqual.o basqual.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 simqual.o -MD -MP -MF .deps/simqual.Tpo -c -o simqual.o simqual.c mv -f .deps/fetchseq.Tpo .deps/fetchseq.Po 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 diffstr.o -MD -MP -MF .deps/diffstr.Tpo -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c mv -f .deps/splitmates.Tpo .deps/splitmates.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 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 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 mv -f .deps/mixreads.Tpo .deps/mixreads.Po mv -f .deps/basqcol.Tpo .deps/basqcol.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 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 mixreads mixreads.o ../src/libseq.a -lz mv -f .deps/simqual.Tpo .deps/simqual.Po 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 basqcol basqcol.o basqual.o ../src/libseq.a -lz mv -f .deps/simread.Tpo .deps/simread.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 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 -j8 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 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 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 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 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 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 ../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) | ~~~~~~~~^~~~~~~ ../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/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-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-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-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-threads.Tpo .deps/smalt_Xali_test-threads.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-insert.Tpo .deps/smalt_Xali_test-insert.Po mv -f .deps/smalt_Xali_test-resultpairs.Tpo .deps/smalt_Xali_test-resultpairs.Po mv -f .deps/smalt_Xali_test-smalt.Tpo .deps/smalt_Xali_test-smalt.Po mv -f .deps/smalt_Xali_test-menu.Tpo .deps/smalt_Xali_test-menu.Po 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 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 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-examples' in '../smalt-examples_0.7.6-9_all.deb'. dpkg-deb: building package 'smalt' in '../smalt_0.7.6-9_arm64.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-9_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../smalt_0.7.6-9_arm64.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/24436 and its subdirectories I: Current time: Sun Aug 15 01:30:03 -12 2021 I: pbuilder-time-stamp: 1629034203 Sun Aug 15 13:30:11 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink15-arm64.debian.net. Sun Aug 15 13:30:11 UTC 2021 I: Preparing to do remote build '2' on codethink15-arm64.debian.net. Sun Aug 15 13:41:06 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. Sun Aug 15 13:41:06 UTC 2021 I: smalt_0.7.6-9_arm64.changes: Format: 1.8 Date: Fri, 03 Jan 2020 11:44:39 +0100 Source: smalt Binary: smalt smalt-dbgsym smalt-examples Architecture: arm64 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: 97b7e01b8f0642f7f0ec60ea14a56f709429a5f4 379380 smalt-dbgsym_0.7.6-9_arm64.deb 675bff33b31fbae6858413b7d86bdc694fdeba29 71870924 smalt-examples_0.7.6-9_all.deb bb5aa6ce1e77d6806076f966fccfb3c84a157524 6219 smalt_0.7.6-9_arm64.buildinfo 6083ea41801b80ad45132ec9ec901f00ea6bb132 103644 smalt_0.7.6-9_arm64.deb Checksums-Sha256: f7e0efe80176562b6e5bf03a0656de651ce1da443a330c69102ed39d946b5506 379380 smalt-dbgsym_0.7.6-9_arm64.deb 7994a25339f0990ad4941c9f880a0cb3ad21ec9af602211fb02c8d84c8a561fb 71870924 smalt-examples_0.7.6-9_all.deb b950dc90c18d301307a4f7421d191913c4d053d050f45bdb8fd9982425164763 6219 smalt_0.7.6-9_arm64.buildinfo 8cf1b48ced7bd2405866b0761c786450c23feeccf440354e8cb19ff67b0d58c6 103644 smalt_0.7.6-9_arm64.deb Files: 9d1dd3bc6a23185c7afd5a62992112a9 379380 debug optional smalt-dbgsym_0.7.6-9_arm64.deb 545dd5558d7479db8b5e69e2e00f9118 71870924 science optional smalt-examples_0.7.6-9_all.deb 35bec9915c586d709627a2d7015da5ba 6219 science optional smalt_0.7.6-9_arm64.buildinfo e2dbb448a270ce7091cfe14f6c1826b2 103644 science optional smalt_0.7.6-9_arm64.deb Sun Aug 15 13:41:07 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.rVSPVMP5a0/smalt_0.7.6-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.rVSPVMP5a0/smalt_0.7.6-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.rVSPVMP5a0/smalt_0.7.6-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.rVSPVMP5a0/b1/smalt_0.7.6-9_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.rVSPVMP5a0/b2/smalt_0.7.6-9_arm64.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: 0.883s) 0.883s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.644s) 0.644s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Aug 15 13:41:11 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Aug 15 13:41:11 UTC 2021 I: smalt from bullseye built successfully and reproducibly on arm64. Sun Aug 15 13:41:12 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Aug 15 13:41:12 UTC 2021 I: Submitting 8.0K b1/smalt_0.7.6-9_arm64.buildinfo.asc Sun Aug 15 13:41:14 UTC 2021 I: Submitting 8.0K b2/smalt_0.7.6-9_arm64.buildinfo.asc Sun Aug 15 13:41:15 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Aug 15 13:41:15 UTC 2021 I: Done submitting .buildinfo files. Sun Aug 15 13:41:15 UTC 2021 I: Removing signed smalt_0.7.6-9_arm64.buildinfo.asc files: removed './b1/smalt_0.7.6-9_arm64.buildinfo.asc' removed './b2/smalt_0.7.6-9_arm64.buildinfo.asc'